The station had two sections: a Strategic Homeport in Stapleton where ships docked, and a larger section occupying Fort Wadsworth, where administrative offices and bachelor and family housing were located.

Comprising about 266 acres (108 ha) with some 280,000 square feet (26,000 m2) of office space, the naval station was also home to NAVRESSO, the Navy Resale and Services Support Office, commanded by Admiral Squibb.

Naval Station New York (Staten Island) was recommended for closure under the 1993 Base Realignment and Closure Commission, as it was deemed too small, too expensive to house personnel, and made unnecessary with cuts to the Navy.

Fort Wadsworth was turned over to the Department of the Interior in 1995 and is administered as part of Gateway National Recreation Area.

The area around the pier is being converted into a mixed-use waterfront neighborhood called Stapleton Homeport.