The 2nd Ave Subway is under construction and will be open next decade (hopefully). Other rail projects in the region of note:
ARC rail tunnel between NJ and Penn Station (under construction)
East Side Access tunnel for LIRR to Grand Central (under construction)
JFK Rail Link from Lower Manhattan (on hold indefinitely)
Extension of the 7 Subway to Hudson Yds (on hold)
Hudson-Bergen Light Rail extension to 8th Street in Bayonne (under construction)
Newark-Elizabeth Rail Link (planning, on-hold)
Northern Branch Light Rail (EIS)
Cross-Harbor Freight Rail Tunnel between Jersey City and Brooklyn (EIS)
Lackawanna NJT Rail Extension (EIS)
West Trenton Line commuter rail service (planning)
Meadowlands Rail Spur (recently completed)
Extension of commuter rail in CT to Westerly, RI and to Springfield, MA (EIS)
42nd Street Light Rail (a dream)
Reactivation of Red Hook Streetcars (planning)
North Shore Staten Island Light Rail (planning)
And lots of new stations, station renovations/overhauls, etc. Some of the more notables include:
Fulton Street Station
WTC PATH Station
Harrison PATH Station
The Staten Island Ferry is actually not operated by the same agency. The MTA operates subways, buses, LIRR and MNR. The SI Ferry is operated by NYCDOT, the agency responsible for the city's streets, bike lanes, etc.
I also like the Roosevelt Island Tramway:
world.nycsubway.org/Around New York/Roosevelt Island Tramway
There have been proposals to develop a more modern tramway between South Ferry and Governors Island, and continuing to Red Hook, Brooklyn:
http://graphics8.nytimes.com/images/...gondola583.jpg
http://graphics8.nytimes.com/images/...s/gov.span.jpg