The towers in the A Division are all considered to be Master Towers (except for those noted as satellites and those that only control a yard)

240 St Tower - located in the yard - controls from 242 St south to the switches south of 103 St that govern the moves into and out of M Track. Also controls both 240 Yard and 137 Yard.
137 St Satellite - located at north end of northbound platform - can control the area both north and south of 137 St.

239 St Yard - controls only the yard and yard leads. I am not sure if this will be taken over by Unionport, but I doubt it.

Unionport Master Tower - located in Unionport Yard - currently controls the mainline switches south of 219 St and the mainline switches between 238 St and 241 St (formerly controlled by 239 St Mainline) and the switches in Unionport Yard (east of the mainline).　 It controls from south of Jackson Ave to White Plains and Dyre Ave.

E.180 Tower - located between 3 Track and M Track just north of the station - controls from south of Jackson Ave to south of Bronx Park East, as well as the entire Dyre Ave line. Also controls the yard at E.180 St (west of the mainline). It has been replaced by Unionport Tower and is now demolished.
Freeman St Satellite - located at north end of southbound platform - can control the area just north of Freeman St.

205 St Tower - located in Mosholu Yard - controls the Jerome Ave line from Woodlawn to north of 167 St, as well as Mosholu Yard.

Westchester Master Tower -located in Westchester Yard - controls the Pelham line from Pelham Bay Park to just south of 3rd Ave/138 St, as well as Westchester Yard.

Mott Ave Tower - located on the mezzanine level between the upper (4) and lower (2/5) levels -　controls from north of 149St/Grand Concourse on both levels to south of 138 St on the Lexington Ave line and south of the station on the White Plains line.

Lenox Tower - located at south end of 148 St Station - Controls from south of 110 St/ Lenox Ave to Lenox Terminal, as well as Lenox Yard.

Times Square Mainline - located on the mezzanine level at the south end of the station - Controls Broadway from north of 96 St to north of Chambers St.　 96 St Satellite - located at north end of station, next to southbound fare control area -　 can control the 96 St interlocking.

Grand Central - located between 3 Track and 4 track south of the station - controls from north of 125 St to south of Brooklyn Bridge, Brooklyn Bridge Loop and Yard, as well as 1 Track and 3 Track of the Shuttle.
125 St Satellite - can control north and south of 125 St
Brooklyn Bridge Satellite - can control loop and yard.

Nevins Tower - located between 2 and 3 Track - Controls from south of Rector St and south of both Wall Sts to north of Atlantic Ave.
Bowling Green Satellite - can control the crossover between 1 & 4 Tracks south of Rector St, the diamond crossover between Wall St and Bowling Green and both the inner and outer loop at South Ferry.

Utica Tower - located on mezzanine outside fare control at south end of station　 -　 Controls from south of Eastern Parkway to Flatbush Ave and Utica Ave. Flatbush Ave　 usually controls the interlocking just north of the station.

Livonia Tower - located in Livonia Yard - Controls from north of Junius St to New Lots Station and Livonia Yard.

Times Square Queens - located at north end of Flushing Line platform - Controls from Times Square to north of Hunters Point Ave.

Queensboro Master - located south of station - Controls IRT/BMT crossover (plus a lot of B div)

111 St - located south of 111 St - controls from Main St to south of 33rd St.

Corona Yard - located in the yard - controls all of Corona Yard and the yard leads
　
　

There are a handful of Master Towers in the B Division, but this is still the home of the single Interlocking Tower.

207 St Master Tower - located in the yard - Controls from　 south of 168 St to 207 St Station; 207 Yard leads north of Dyckman St and 174 St Yard.
168 St Satellite - can control 174 St Yard and 168 St interlocking.

59 Master - located north of northbound platform at 59 St - controls from north of 145 St to south of 59 St.

DeKalb Master Tower - located on mezzanine behind token booth - Controls Lawrence St interlocking on B'way local line; Gold St interlocking (between DeKalb and the Manhattan Bridge Portals; DeKalb Ave to　 north of Pacific St on Fourth Ave and to south of Prospect Park on the Brighton line, as well as all of the Franklin Shuttle. Also has control of the wheel detectors on both sides of the bridge.

Joe Murphy Master Tower - located in 36 St/38 St Yard - Controls Fourth Av Line from north of 36 St to 95 St; West End line from 36 St to the connection to NYCHRR and 36 St/38 St Yard; Sea Beach interlocking at Sixth Ave. This tower will eventually control the West End line to just north of Bay Parkway.

Stillwell Tower(Tower B) - located in Coney Island Yard - Controls Stillwell Yard and Coney Island Yard, but not Culver (City, Avenue X) Yard; Sea Beach line from Stillwell to north of Kings Highway; Brighton line from Stillwell to south of Kings Highway; Culver interlocking south of West 8th St (part of Stillwell Station - allows choice of pocket). When signal upgrade is complete, will also control West End from Stillwell to Bay Parkway (with a satellite at Bay Parkway).

City Hall Tower - located at north end of station - Controls the Broadway BMT line from Lexington Ave/59 St to the Nassau St cut in the Montague tubes, as well as the mainline and relay switches south of Broad St.
57/7 Satellite -located at south end of southbound platform - can operate interlockings north and south of station. This satellite is active for the duration of Q termation at 57/7.

Essex Tower- located at Essex St opposite side of J1 track from platform (next to old trolley terminal) - Controls Nassau St line from the Brooklyn side of the Williamsburg Bridge (wrong-rail blind trips and normal direction wheel detectors) to north of Broad St and the Sixth Ave line from north of B'way/Lafayette to south of Delancey St.

East New York Master Tower - located in east New York Yard - Controls the Jamaica　 line from Marcy Ave to Jamaica Center (lower level); the Myrtle Ave line from Myrtle to Metropolitan Ave; the Canarsie line from south of Broadway Junction to north of Livonia Ave; East New York yard leads; the Linden Yard lead south of Livonia Ave and the switch between the lead from the Livonia Ave el and the Canarsie lead.
Parsons/Archer Satellite normally controls from north of 121 St to Jamaica Center.

Queensboro Master Tower- located south of the station on the structure - Currently controls the IRT/BMT crossover; the Astoria line from the 11 St cut to Ditmars Blvd; the 63rd St Connector from south of Lexington Ave/63 St to 36 St, including all entrances to D5 Track; and Crosstown line south of Court Square. When completed, this fully computerized Tower will control the above plus - the Crosstown line from south of Bedford/Nostrand to Queens Plaza; the Queens Blvd line from south of Ely Ave to north of Roosevelt Ave (possibly farther, I don't remember); the entire length of the Flushing line. In all actuality, the model board shows all of this trackage, but since the controls are all computerized, it's very hard to tell the extent of control.
21 St Satellite - can control the area from north of 21 St to south of Lexington Ave/63 St

Liberty Junction - located on the structure between K1 and F4 Tracks - controls from Liberty Junction to both Lefferts Blvd and Broad Channel.
Lefferts Satellite - located at the north end of the platform - controls Lefferts Terminal
Howard Beach Satellite - located behind the station wall of the northbound platform - can control the area north and south of the station.

Bedford Park Master Tower - controls the Concourse Line from 205 St to south of 161 St, putting six interlocking towers out of business.

Unless otherwise noted, these towers control only the interlocking closest to their location.

Canarsie Line
8th Ave/14 St - at south end of platform in Dispatcher's Office
3rd Ave/14 St - at north end of northbound platform
Bedford Ave - at south end of platform
Myrtle Ave -　 at south end of platform
Rockaway Parkway - at north end of platform - controls from south of 105 St to terminal and yard leads

Crosstown Line
Court Sq - south end of platform
Bedford/Nostrand - north of northbound platform on opposite side of E2 Track
Nassau Ave - north end of northbound platform
these will be taken over by Queensboro Master when signal upgrade is complete.

West End Line
8th Ave - located in 38 St Yard - controls 9th Ave station and crossover between D3 and D4 Tracks in the mini-tunnel.
62nd St - south end of northbound platform
Bay Parkway - south end of northbound platform
Tower D (Bay 50th) - located behind northbound platform wall - controls all switches on either side of Bay 50th St station and the switch on the leads closest to the tower
The last two towers will be taken over by Stillwell Master when signal upgrade is complete, the first two by Murphy Tower.

Culver Line
Tower C - located in CI Yard between southbound mainline and yard lead - controls Ave X, yard leads and Culver Yard.
Kings Highway - located at south end of southbound platform
Church Ave - located at south end of southbound platform - controls from south of Church to south of Ditmas and Church Ave Yard
4th Ave - at north end of northbound platform
Bergen Street - at north end of upper level northbound platform –Now closed. Control transferred to Jay Street Master Tower
Jay St - at north end of northbound platform
York St - south of south end of platform

6th Ave Line
5th Ave - south end of southbound (upper level) platform - controls split/merge between 6th Ave and 8th Ave service and diamond crossover north of Lexington Ave
50 St (Rockefeller Center) - at north end of northbound platform - controls Rock Center and diamond crossover south of 57 St. This tower is no longer manned, resulting in the wonderful "What you punch is what you get" admonition to Train Operators. Any wrong line-ups here are solely on the TO.
34 St/6 Ave - located north of northbound platform
W. 4th St - at south end of southbound lower level platform - controls all switches north and south of the station.

Concourse Line
205 St - at south end of platform *
Bedford Park - at south end of southbound platform *
Fordham Rd　 - at south end of southbound platform *
Tremont Ave - at south end of southbound platform *
167 St - north of southbound platform *
161 St - at south end of southbound platform *

* Bedford Park Master tower is now operational and these towers are closed. The new master tower is located in the station mezzanine

Queens Boulevard Line
179 St - north end of northbound platform - controls from north of 169 to terminal and relay tracks
Parsons Blvd - north end of northbound platform
Parsons/Archer - north of station on lower level -controls both P/A interlockings as well as Jamaica/Van Wyck and Van Wyck Blvd. Lower level interlocking can be remotely operated by ENY Master
Union Turnpike - north end of northbound platform - controls north and south of station as well as the yard lead up to Jamaica Yard portal
Continental Avenue - north end of northbound platform - controls north and south of station as well as the relay tracks and yard lead up to Jamaica Yard portal
Roosevelt - north end of northbound platform
Queens Plaza - north end of northbound platform - controls north and south of station, 11 St cut and Ely Ave
These last two will be taken over by Queensboro Master when signal upgrade is complete.

8th Ave Line
World Trade Center - north end of platform
Chambers St (8th Ave) - north end of platform
Canal St - south end of southbound platform
30 St/8th Ave - located south of 34 St on the southbound side near the crossover between A1 and A3 Tracks
42 St/8 Ave - I admit to confusion on this one. The schematic shows two towers　 - one north of the northbound platform and one south of the southbound platform. I think that the northern one, which is manned, controls all switches north of the station, while the southern one controls the merge of the lower level track onto the mainline.

Fulton St/ Rockaways Line
Court St (Museum) - north end of platform
Hoyt St - south end of the abandoned southbound platform
Lafayette Ave - south end of southbound platform
Utica Ave - south end of southbound platform
Broadway/ENY - south end of southbound platform
Euclid Ave - south end of southbound platform - controls north and south of station as well as the first diamond crossover on A5/A6 yard leads (used for relays)
Pitkin Yard - located in the yard - controls the yard, yard leads and mainline from north of Grant Ave to north of 88 St
Rockaway Park - located at north end of platform - controls Rockaway Park Yard and Hammels Wye, as well as the approaches to the South Channel Swing Bridge. Hammels Wye Satellite - located between F4 and F3A Tracks - can control all interlockings associated with the Wye.
Mott Ave (Far Rockaway) - at north end of platform

Yards
207 Yard - controlled by Tower A (south end of yard) and Tower B (north-west corner)
Concourse Yard - controlled from Tower located in Yard
Fresh Pond Yard - controls yard leads and Metropolitan Ave
All other yards not mentioned somewhere above are hand-throw yards and are NOT controlled by a tower.

Notes
All of these single interlocking towers cannot necessarily be seen from the platform, eve though they are listed as being at the end of a platform. They are also not necessarily manned 24/7.
The model boards at the master towers and the terminal Dispatchers are capable of "seeing" a larger area than they actually control.

Sometime in the future, we will see more Master Towers springing up. My guesses for some of them:
Canarsie line Master Tower - will control the entire length of the Canarsie Line - will be made necessary for CBTC operation.
Fulton St Master Tower - to control the Fulton St line from Hoyt/Schermerhorn to north of 88 St.
Stillwell Master Expansion - to control the Culver line from Kings Highway to Stillwell Ave.
Jay St Master - to control from Church Ave/Culver to York St.
Jamaica Master - to control from 179 to the eastern end of Queensboro Master.
Queensboro Master Expansion - to control from 5th Ave to Ely Ave.
59 Master Expansion - to control from 30 St/ 8th Ave to 59 St and to control Rockefeller Center to 59 St.
West 4 St Master - to control from 34/6 to W. 4 St and W.4 St to Chambers St /WTC

This page is subject to change as master towers become operational and/or local towers are eliminated and/or consolidated.

Updates and corrections are always welcome