Bay Ridge, Brooklyn
The Circumferential Line is proposed to begin in Bay Ridge, where the LIRR Bay Ridge Freight Line has a lighterage dock along the Brooklyn waterfront.
Although the proposals for the transit line seem to have it terminating in the Bay Ridge rail yard, it might make sense to extend it just a few hundred feet further to wrap around the back (west side) of the Brooklyn Army Terminal and connect with the ferry landing on Pier 4. Maps show that there were tracks extending to the Army Terminal Piers and with some upgrade and electrification, they'd be good to go.
While the current NY Water Taxi service is completely directed at commuters with a very limited number of runs in the morning and afternoon, addition of a station from the Circumferential Line would make it more readily accessible to a large number of new, potential riders that wouldn't mind shaving a few minutes off their commute to downtown Manhattan. The long-term end result could be similar to what happens now with the South Ferry (1 train) connection to the Staten Island Ferry in Battery Park on the southern tip of Manhattan.
When the Bay Ridge Line was built in 1876, this was a busy passenger ferry terminal connecting Bay Ridge to lower Manhattan, which was then the heart of New York City. Passenger service ended on the Bay Ridge line in 1924, although this remained a yard for the freight line. The yard was abandoned during the 1980s and 1990s before being renovated and reopened in 1999 as a storage, switching, and intermodal transfer yard.
The yard is also used by rail cars that are floated across the bay by the New York Cross Harbor Railroad, which uses the old Bush Terminal carfloat apron at the foot of 50th Street to the north and brings the cars down First Avenue and through the Brooklyn Army Terminal to the 65th Street Yard. The NYCH had a plan in the late 1990s to move their operations to the 65th Street yard and rebuilt the 65th Street floatbridges to handle the larger railcars being used at the time. However, the move never took place and the floatbridges at 65th Street remained unused.
There has been a proposal in the works for a number of years to dig a new freight rail tunnel under New York harbor to connect the Greenville Branch in Jersey City to the Bay Ridge line. Rail cargo from the south and west currently must either be offloaded to trucks in New Jersey (further clogging NYC's roads and bridges) or sent further up the river to the closest Hudson River crossing at Selkirk. The eastern portal of the tunnel would be to the west of the Bay Ridge Yard, probably between 8th and 13th Avenues.
Consideration has also been given to a tunnel that would provide a subway connection to Staten Island.
Given the waterfront isolation away from residential property (or potentially developable property), a better western terminus for the Circumferential Line might be under Towers of Bay Ridge, a group of oddly out-of-character high-rise residential buildings built in 1972. The parking lot for the buildings was built on a platform over the Bay Ridge Line tracks and there is probably space under the platform for a station of some kind.