I don't think any of Disney's hotels have an indoor pool. You may have to look off-property. However, Disney does heat their pools and you can't beat being on-site.
You might want to look into:
Embassy Suites Lake Buena Vista
Embassy Suites International Drive South
These look like the only hotels in my book that list indoor pools as an amenity. All other resort/hotels only list outdoor pools.
Hope this helps!