There is absolutely a bridge or tunnel that takes a train to Queens. Its called Hells gate. Or the East River tunnels if you're ok with routing your freight ops through Penn Station (massive short cut).

One of those mostly invisible things people don't know about is the New York and Atlantic Railroad, which is basically a private group that has been contracted to take over the freight operations that were previously run by the Long Island Rail Road. You can see some of their locomotives in the picture.

The short line connecting railroad mentioned sounds like its the NY&NJ, which is actually a barge float operation between the 65th st yard and Bayonne iirc. There are certainly ways to avoid this barge, but they are rather circuitous, and could only maybe be done at night otherwise the slow freight trains would get in the way of normal passenger service on those tracks.

And describing an extra siding on the Bay Ridge Branch as a "new terminal" is a bit misleading.