Even the larger boats that go between WL and MK are not always accessible to scooters or power wheelchairs. It depends on the water level. If the water level is too high or too low, the boat will be floating too high or too low compared to the dock.
The boats at the Epcot resorts are usually not affected by water level because their docks are somewhat different and they are on smaller waterways (that have the water level controlled better) than the large Bay Lake that WL is located on.
There are more details about this on the FAQs thread stuck to the top of this board.
If you stay at one of the Epcot resorts, you will also be able to walk (or roll) to Epcot and the Studio.
If you stay at one of the MK Monorail resorts, you can avoid the boats and the buses by taking the monorail to MK and Epcot and taking the Epcot boats (or walking/rolling) to the Studio.