Troop NYC is still in operation but their structure is different then the other troops. Troops A, B, C, D, E, F, G, H, K, L, & Thwy are subdivided into Zones by counties that they patrol. These Zones are responsible for both patrol & investigations from various sub-stations.
Troop NYC Headquarters has been moved to 36 Thomas St in lower Manhattan from Wards Island.
Zone 1 - headquarters is located on Wards Is on the grounds of the state hospital. These troopers are responsible for patrolling transportation hubs, Penn Station Grand Central Terminal, JFK & LGA airports and other important facilities.
Zone 2 - works out of 99 Tenth Ave in Manhattan & is part of the NY Drug Enforcement Task Force. At one time they also had troopers assigned to various other investigative units including District Attorney Squads, Federal Task Forces, & so on.
Zone 3 - covers the highways besides the bridges & tunnels. They work out of five substations
:
Bronx - Throggs Neck Bridge (Bronx side)
Brooklyn - Hugh Carey Tunnel / Brooklyn side at 160 Hamilton Ave.
Manhattan - Downtown - 36 Thomas St (also Troop HQ)
Queens - aka Station Rockaway located at the Brooklyn foot of the Marine Pkwy Bridge off of Flatbush Ave
Staten Is - located with in the plaza area of the VZ bridge, Bklyn bound side.
I hope this answers your question. They are here & it looks loke they are staying.