Jamie:
When we stayed at Fort Wilderness in January, right across Bay Lake from
Wilderness Lodge, I noticed that they were running the larger boats (that allow you to leave your strollers open because their gangway is the same height as the dock) for the trips back and forth to the Magic Kingdom. However, the smaller boats were still in service for the route that makes the loop to Fort Wilderness, the Contemporary Hotel and back to Wilderness Lodge.
Boat itineraries can change, so before you head down to the lodge's dock, confirm this at the front desk. If they are not running the larger boats, they will be running a bus because guests in wheelchairs are also at a disadvantage when the smaller boats run. Either way, you should have an option that allows you to keep your stroller open.
Wishing y'all a magical vacation!
Whitney