I've not stayed in a cabin at Fort Wilderness, but have visited (Hoop de Doo, lunch/dinner at Trails End, petting farm, horseback riding), but I have stayed at HIFS. I can't address which accomodation would be most comfortable based on your family's size.
However, I think there is more for you children to do at HIFS than at Fort Wilderness (in my opinion). For example, the petting zoo does not take that much time. Some of the other Ft. Wilderness activities, horseback riding, carriage rides, have additional fees. Based on the ages of your children, the pony rides are not an option. In addition to the themed pool (however, no water slide), HIFS has an arcade room, free evening activities (face painting, karaoke, etc), and now offers salon/spa services for girls.
If going back to the hotel in the afternoon to rest is a consideration for your family, you will be able to do this easily staying at HIFS. It takes no more than 10 minutes (maybe a little less) from HIFS to the Magic Kingdom. If your destination is MGM/Studios or EPCOT, HIFS is much closer.
If you opt for the cabin at Ft. Wilderness, you will find it easier to get about if you have car.
Take a look at the Orlando Hotels and Attractions board for more info about HIFS and the Camping at WDW board for more info about the cabins.
Regardless of the accomodation you choose, have a wonderful vacation!