Polynesian is one of only two (or three?) hotels with a zero-entry pool. This means that at one end, you can wheel your son into the water, just like at a beach. The Polynesian has waterproof plastic wheelchairs for that purpose. None of the moderate or budget class resorts have zero entry pools. All the other resorts will have at least one pool with what I call 'bump steps" where your son can bump himself out of the water on his backside one step at a time onto a wheelchair height platform.
If you are not renting a car during your visit, The Polynesian is the closest (walking distance) Hotel to the Ticket and Transportation Centre (TTC) where you can pick up a Lynx (Orlando public transport) bus direct to Sea World. Lynx buses have wheelchair lifts. You can also use Lynx to get to universal, but you have to change buses.
The Wilderness Lodge is also fun for younger guests, especially the Roaring Forks restaurant. However, it doesn't have a zero entry pool. It is however, only a short bus ride away from the Polynesian if you want to visit for a meal. Fort Wilderness, also nearby, has a fun dinner show called 'Hoop de Hoo', a petting zoo, and an outside barbecue and film show, which youngsters would enjoy.
The polynesian restaurant also has entertainments provided by the wait-staff geared to younger visitors.
The Polynesian is a good choice especially if your son is at the age to enjoy the Magic Kingdom. If he is older, and doesn't need a zero entry pool, Beach Club/Yacht Club and Boardwalk are also good choices because access to Epcot and MGM are so good.
Andrew