Lots of points for waterside interchange. A lot cheaper to put it on a barge, push it to the destination, be it a Terminal in the Bronx, a pier station in Manhattan, alongside a ship in the harbor or a rail yard in Brooklyn.
You could own a bunch of barges and then only need a few tugs to move things around.
At the time there were lots of locations a freight car on a barge could go. Car ferries work best over a fixed point to point route.
Since there is only one route now, someone did propose a RO-RO (roll on - roll-off) service a decade or so ago using a car ferry.