Piece of Cake! The Friendship Boats are easy to get scooters and wheechairs on and off of. DS uses a mnaul wheelchair and we inevitably board a boat at DHS or Epcot with 2-3 scooters and wheelchairs, in addition to lots of strollers. Proper boarding is through the back as there is an open area inside specifically for scooters and wheelchairs.
We own DVC at the Boardwalk, so we ride these boats very frequently. We have always found them far easier than the buses, since there's so much more room aboard.
Good luck!