Totally agree with the duck and boat rides. The natural landscape is amazing. I think the Upper Dells tour where you can get out and walk a bit is the best. Also, Devil's Lake State Park has alot of natural beauty (and a lake, hiking, picnic and swimming areas). H.H. Bennett Photography Studio also has some great historical perspective- http://hhbennettstudio.wisconsinhistory.org/
IMO Tommy Bartlett watershow is a classic Wisconsin tradition when in the Dells and the night show is the best.
For restaurants, Moosejaw Pizza & Dells Brewing Co. is a popular family favorite and ask how to get to Ravina Bay Bar & Grill. It is on Lake Delton right across from Tommy Bartlett watershow. Food is good and the location is great if you eat outside on the deck overlooking the lake. We had fun watching two sets of mama ducks and all their little babies come on shore while we were there last summer. Mexicali Rose is a good mexican food restaurant.
House on the Rock in Spring Green almost defies description. If you have time, it will definitely be a one of a kind experience and there is something for everyone. The house itself is cool- on the edge of a cliff that you can walk out over the edge, and a tree growing in through the house. But the "collections" are beyond compare. Almost a sensory overload. The Colliope collection and the Merry-go-round are definitely something you won't see anywhere else. http://www.roadsideamerica.com/story/2254
You will have fun no matter what you choose to do!