We stayed at the Wilderness Lodge in The Dells and it was great. I think there are 3 separate indoor waterparks, as well as a huge game room and indoor play/climb area. They have crafts and other activities as well. You can stay in a regular hotel room, or you can choose a condo. We did the condo because you get a full size kitchen which is nice because you can make your coffee in the morning, have cereal for breakfast instead of paying $30 to eat out, and have lunch in your room as well. I loved it, because after swimming all day, the last thing any of us wanted to do was sit in a restaurant. The condos also have a family room separate from the bedroom. Meaning - you and the hubby can relax and watch some tv, have a glass of wine, unwind without disturbing your son.
If he loves animals, there is a deer park www.wisdellsdeerpark.com where the deer will literally eat out of your hands. I have pictures! ;) It's pretty cheap and I think you can find coupons online.
Have a great trip!