Is the ferry privately owned? If so, they morally (if not legally) have the right to bar firearms.
The federal law is designed to protect transporters of firearms from State laws when traveling from one location where possession is permitted to another such location. It does not supersede other federal laws or private property rights.
If the ferry is State- or local-government-owned and if there is no federal law barring carry on the ship or no federal law allowing for the regulation of carry on the ship, then carry should be protected by the federal law protecting transportation of firearms.