The pool at your Resort may be a great place to spend time - and most pools should have a lift for your son to transfer in and out.
Pin trading - any CM should be happy to trade, and every Resort has a pin trading board (typically in the shop)
Smashed pennies - machines are all over WDW (including in many/most Resort lobbies & Disney Springs) and they make a great, inexpensive - and easy to pack! - souvenir.
Ride the Monorail loops - both of them - just for fun!
Boat rides - with your son's wheelchair, the rides from GF/Poly to MK are out, BUT every other boat route at WDW is accessible (WL + FW boats alternate, so you may have to wait a bit). We like them all - from FW/WL to MK, then take the
BUS to HS, and ride the round trip from HS through the Resorts to Epcot
on the Friendship boats. There's also several routes at Disney Springs - you can ride from one end of DS to another, or ride to OKW (Olivia's has great food any time of the day!) or there is a route that goes to and from POFQ/POR. POR has Yee-Haw Bob in the evenings for some great family fun!
Disney Springs typically has street musicians and performers in the evenings if your family enjoys that kind of thing.
Many of the Resorts still have the (free) movies on the lawn every night (weather dependent) and many of them also have S'mores campfires (buy the kits in the Resort store)
Every Resort has an Arcade, BTW; some are surprisingly big, and almost all of them are always nearly empty (except during hurricanes LOL)
In the Parks, you can also look for smashed penny machines and pin trading opportunities. There are many "museums", movies or exhibits (especially at WS) that are great if you have someone who might need to opt out easily. Canada, France & China at WS all have movies. Japan, Morocco and Norway have little museums tucked away, and China has a fascinating exhibit as well. The Mexico pavilion regularly updates their exhibit. As HS, One Man's Dream has been renamed, but still contains an exhibit featuring Walt Disney's history. There is a great Star Wars exhibit over in the Launch Bay with actual props from the movies.
At MK, the Grand Circle tour on the train is a huge favorite of ours as well!
edited to add clarification re: Friendship boats
edited JUST FOR @katyieeldr LOL: changed monorail to BUS