The Disney Springs area (Sassagoula River) boats are all pontoon boats:
They can take wheelchair/ECVs - up to two with roll-on ramps and designated spaces behind the captain with fold up chairs.
The Bay Lake area (MK and related resorts) use these larger boats which have enclosed spaces and outside seating back and front and can accommodate all types of wheelchair or
ECV:
The MK resorts are occasionally serviced by the smaller canopy boats - often you'll find these on the Poly/GF run, and the Fort Wilderness run:
These cannot accommodate wheelchairs or ECVs - they have no space for roll-on, no ramps, only stairs inside the boat, and very narrow aisles. Some resorts may be serviced by both the larger and the smaller boats - depending on time of day and crowds.
The boats that go from Hollywood studios to Epcot (FriendShip), and stop at Swan & Dolphin, Beach & Yacht, and Boardwalk, are large mostly inside-seating boats with ample roll-on space for ECVs and wheelchairs:
These are also the same types used inside Epcot's World Showcase lagoon.
And of course the ferries between MK and T&T center are huge and can accommodate plenty of ECVs and wheelchairs:
So you're fine with all but the small canopy boats around the Bay Lake area. I'd definitely ask personnel at the dock what type of boat is being used if you're unsure and they can let you know if the canopy boats are the only ones available - so you could switch to a bus or monorail if needed.