Hi Will!
We stayed at just the resort and and really enjoyed it, so I can imagine how much fun staying at one of the villas must have been. Animal Kingdom is definitely at the top, as my son (at 5) loved looking out the window and seeing the various wildlife.
But to highlight a few others...
Disney's
Coronado Springs was a good locale for my children. If for no other reason, they have a massive Dig Site with a kiddie pool area, as well as a pretty good sized playground next door.
Disney's
Polynesian,
Caribbean Beach, and
Grand Floridian have nice sized beach areas you can walk out and enjoy. Our kids loved the feeling of being at a beach with the resort in close distance.
The
Contemporary was another highlight. My son couldn't get over seeing that monorail shooting through "the building." If you stay here though, make sure to get the Theme Park view, you won't be disappointed.
So take a look at the links and see if the amenities are something your family could enjoy. Good Luck!