When I was at NYCTA Track & Structures in the 1980s, we received most of our track materials at 38th Street Yard via the NY Cross Harbor RR. One spring their barge lost several gondolas of rail (including our entire order of heat-treated rail) into Gowanus Bay. For a couple of weeks, there was a crane with an electromagnet on a barge out in the bay, fishing for our rail. I don't know how much of it they found.
We also had a track connection at Linden Shop, which is adjacent to the Canarsie Line. I don't know if the 38th Street connection is still active, but I'm sure the Linden Shop one is. When a contractor was assembling new cars in the Brooklyn Army Terminal, they were moved on their own wheels up the Bay Ridge Branch to Linden and onto NYCTA that way.
There used to be a track connection into East 180th Street Yard in the Bronx, as well, but that was inactive 25 years ago and may be gone entirely now.
As for trucking subway cars, I remember the R-62 and R-62A orders coming in on flatcars via NY Cross Harbor. The Redbirds moved out the same way. In fact, there was even an excursion that went onto the SBK trackage a few years back, so maybe the 38th Street connection (which involved an at-grade crossing of 3rd Avenue) is still active.
Randy Resor, aka "NellieBly" passed away on November 1, 2013. We honor his memory and his devotion to railroading at railroad.net.