Sean, I'd suggest Gateway Marina 718-252-8761 in
Brooklyn by Floyd Bennett field. They have parking and are a five-minute bus ride from the end of one of the subway lines that runs up into Manhattan, right off the Belt Parkway. Facilities will be closed in the winter...but you're right off the busy
Brooklyn streets.
Or the World's Fair Marina up in
Flushing, they do have one deeper
dock that might
work for you, and they are open in the winter but AFAIK no official liveboards.
Other than that...either the schlep from City Island or try one of the
marinas on the NJ side, one PATH train stop from Manhattan. (Port Liberte,
Newport, Liberty State Park.)
Then again...the USS Intrepid is being sent out for
repairs very shortly, they'll be a large berth available in Manhattan.<G>