General:
* Vessel
* Craft
* Watercraft
* Ship (though usually larger)
* Barge
Specific types:
* Canoe
* Kayak
* Dinghy
* Yacht
* Raft
* Ferry
* Cruiser
Figurative:
* Ark
* Galleon (for something large and grand)
* Skiff (for something small and light)
The best synonym will depend on the specific situation and the type of boat you are referring to.