Brook tower is no longer a manned tower. Both the block operator and yardmaster have been re-located to inside the Atlantic Terminal crew facilities.
West Side Yard is not so much a tower, as its part a building that houses a repair shop, crew facilities, etc... The control room has the yardmaster and block operator side by side coordinating train movement.
PSCC (Penn Station Central Control) is a building in Manhattan where there are LIRR block operators work with Amtrak dispatchers.
Manned towers would be:
Towers still standing, used by other crafts
Standing, but unused?
Pond tower is now used by NYAR
Locust tower is now used by the Nassau County Police
There are roustabout moves that will contact "Q tower" on their way to Arch Street Yard. That would be an Amtrak tower, but LIRR crews will contact them if going to Arch Street yard.
The mid-day storage yard, just east of Arch Street yard (Northwest of sunnyside yard) is going to house a block operator and yardmaster (so I'm told). The building can be seen looking east from Queens Blvd as it crosses over the yard.