Hi Daphne!
Both the Wilderness Lodge and the Animal Kingdom Lodge are great places to stay; you really can't go wrong with either one. My personal favorite is the Wilderness Lodge. I love the theming. I love the location. I love the atmosphere. I just love this resort and you can get more of my thoughts on the lodge
here.
However, my 5 year old son's favorite resort is the Animal Kingdom Lodge. The theming is incredible and there are animals everywhere. This can be a once in a lifetime opportunity, as a lot of guests will only have this opportunity to wake up in the morning and see exotic animals right outside their window at Walt Disney World The resort has great dining options; Boma is a great family buffet and Jiko is great for adults looking for a quiet romantic evening. There are a lot of activities for young guests at the resort and the pool is fantastic; I have to admit that it is nicer than the pool at the Wilderness Lodge. I also have to admit that Animal Kingdom Lodge's Quick Service restaurant is better than the one at the Wilderness Lodge.
On the other hand, the Wilderness Lodge has a huge advantage in its location. Being on Bay Lake puts it just a boat ride away from the Magic Kingdom. That makes it very convenient to return from the Magic Kingdom for a break, swim in the pool, nap, etc. Animal Kingdom Lodge, on the other hand, can be 45 to 60 minutes away on average from the Magic Kingdom via Disney Transportation. With young children this may be important to you as I think the best parks for young children are the Magic Kingdom and Disney's Hollywood Studios.
It's a hard decision, but you really can't make a mistake with either! Good luck and have a magical vacation!