Yes, The larger boat that goes to Magic Kingdom and Wilderness Lodge from Ft. Wilderness is accessible.
The boats that travel between Epcot, the Studios, and the Epcot Resorts are accessible.
The boats that travel between Downtown Disney, Saratoga Springs, Old Key West, and Port Orleans are accessible.
The small boats that travel between Ft. Wilderness, Contemporary, Wilderness Lodge are not accessible.
The small boats that travel between Magic Kingdom, Polynesian, and Grand Floridian are not accessible.
The large Ferry boats that travel between TTC and the Magic Kingdom are accessible.
The boats that run in World Showcase Lagoon are accessible.