I go up there once or twice a year (though on a lot of those trips, we avoided the waterparks altogether).
Compared to 20 years ago, when most of the tourist attractions pretty much shut down after Labor Day, the indoor waterparks have made it a year-round attraction. Of course, a lot of the popular summer attractions (the Ducks, the boat tours, the go-karts, the Tommy Bartlett show) don’t run during the winter, but a number of indoor attractions have been built.
The big three indoor resorts are the Kalahari, Great Wolf Lodge, and the Wilderness (though a number of other hotels and resorts have built indoor parks, too). All of the big three have extensive indoor water parks, and are sprawling operations (every year, they build more stuff). They’re all good operations, but they tend to be very crowded and loud, particularly on the weekends. The cost of your room at one of those resorts includes waterpark admission; you can also get admission to a waterpark without being a guest at that resort, but you have to buy the admission separately (and they may have restrictions on how many such passes they sell, or when you can use the waterpark).
I’ve stayed at the Kalahari (not bad, but we stayed at the condos, which were, at that time, at the very far end of the resort from the waterpark), and at Wilderness (I like that place a lot). It sounds like you have a fairly big family – if you stay at Wilderness, look at the “Frontier Condos” – they may be a little more expensive than the hotel rooms (which are directly attached to the waterparks), but they’re far nicer, and get you away from the crowds. They have shuttle buses which will come to your condo and drive you to the waterpark (it’s not that far, but not a great walk in the winter with little ones). I’ve never been to Great Wolf, but I’ve heard it’s not bad (probably very similar in quality to the Kalahari).
I’m not sure if there’s a stand-alone indoor waterpark in the Dells – I suspect that there isn’t (or, at least, there hasn’t been). The business model up there for the winter months seems to be to encourage families to check in, and then never have to go back outside / leave the resort.