The CK&S ran parallel to the GTW between King Highway and Mills Street but they did not have a yard there, only the GTW did. Way back when the CK&S was independent their yard must have been north of Paterson St. The LS&MS yard (North Yard) was right along side but neither yard could have very big. They seem to have become one yard apparently under NYC's time.
The original Pennsy yard was between Crosstown and Mills Street but when they needed more they build north of Mosel. That yard was known as Dock but I don't know why it was called that.