The ferry boats to MK are accessible.
Larger boats, known as "cruisers" are usually accessible. Occasionally if the water levels are low they are not and alternative transportation will be available. Cruisers run between MK area resorts.
The Friendship boats that run between DHS and Epcot, as well as the Epcot area resorts, are accessible for wheelchairs and offsite
ECV rentals. I believe onsite Disney rental
ECVs do not fit.
The boats that run between DTD and resorts are accessible.
Smaller boats, known as "launches" are NOT accessible. These run between MK area resorts, and usually alternate with the larger "cruisers" so you may need to wait for the next boat.
Any of the accessible watercraft you should be able to drive/ride directly onto the boat. If using a manual wheelchair, and able to step into the small launches, I believe the wheelchair can be folded and carried on (like a stroller).
Enjoy your vacation!