All Star Music family suites will give you 3 beds in the living room area -- a full-size sleeper sofa, twin-size sleeper chair and the ottoman opens into a twin-size bed. I've heard there isn't much room to move about with all 3 opened, but if the wheelchairs don't need to be immediately beside the kids' beds, you could park them in the bedroom. There are wheelchair accessible suites with either a tub or a roll-in shower, depending on the needs; and the suites have 2 bathrooms so would have a regular tub as well.
AoA family suites have 2 full-size beds in the living area - a sleeper sofa and murphy/table bed - and I think I've read of people putting out a twin-size air mattress as well. But that will take up pretty much all floor space, though I don't know if the wheelchair accessible layout has more floor space, so again the wheelchairs may not be next to the beds overnight.
Other value resorts only offer 2 beds, though you could put an air mattress down for the 3rd. That may or may not take up too much space since you need room for 2 wheelchairs as well.
The Fort Wilderness Cabins have a queen and bunk beds in the bedroom, if either child can use a top bunk. And again I think the wheelchairs would need to park in the other room overnight.
Some of the moderate resorts have rooms that sleep 5, which includes two queens plus a smallish murphy bed (smaller than twin size). If one of the kids would be OK on the murphy, that might be an option. Booking preferred at POR will get you into Alligator Bayou which I believe has the murphy in all rooms; otherwise I don't know if you can guarantee the extra bed as families of 5 will take priority for those rooms.
I'm not as familiar with the deluxe resorts but most allow for 5 guests and include a daybed. Deluxe will have the largest single-room options (other than suites) as far as square-footage, which might be important considering you want 3 beds plus space for 2 wheelchairs. They come with the largest price-tag as well.
Watch the room descriptions. I don't know if "Florida accessible" rooms would have what you need or not; it likely depends how mobile are the kids. "Wheelchair accessible" rooms will have wide pathways in the room (wide enough for a standard whelchair). Some "wheelchair accessible" include a tub and others a roll-in shower, so watch that description as well if the tub/shower area is important for your family's needs. I believe a Communication Kit can be provided for any resort room to accommodate "hearing accessible" features, though in my searches I think I've noticed most (if not all) wheelchair accessible rooms also include option for hearing accessible.
Feel free to ask questions on the
disABILITIES Forum about specifics.