Amber:
No matter at which resort you stay, if you take Disney bus transportation, you will need to fold up your stroller for safety and hold your child in your lap. If you plan on staying at the Fort Wilderness cabins, you won't have to fold up your stroller on the boat launch from Magic Kingdom to the fort's marina, but if you then take the bus from the Settlement area near the marina to your cabin, you'll have to fold it up to board. Walking to the cabin, in my opinion, is not the best option as it is about 1/2- to a mile walk depending on where your cabin is located.
If you're looking to keep your sleeping child undisturbed, consider staying at one of the Magic Kingdom resorts like the Contemporary, Polynesian or Grand Floridan. You don't have to fold up your stroller to ride the monorail to your resort. Best of all, you can access both the Magic Kingdom and Epcot via the monorail. Because the monorail unloads in the lobby of the
Contemporary, I'd give a leg up for convenience to the park and your room.
Wishing y'all a magical vacation!
Whitney