Hi Mary,
You must be so excited for your first Walt Disney World vacation! Both resorts are wonderful in their own way. Wilderness Lodge is a beautiful resort with one of my family's favorite restaurants,
Whispering Canyon Cafe. It's also super easy to get to Magic Kingdom. Art of Animation, on the other hand, is just fun! You honestly feel as though you are part of the movie set. The food court there is incredible. You'll have a great time at either resort.
Having said that, we usually opt to go without a car, so my recommendation is to get as close to the magic as possible. Wilderness Lodge is just a short boat ride from Magic Kingdom. The buses to the other resorts are really quite convenient. Disney Vacation Club (DVC) has two bedroom villas that sleep 8 and include a full kitchen. The price may be a bit high, but you'll have the ability to cook and eat some meals in your resort if you choose. Otherwise, you would have to get two separate rooms to accommodate your family.
If you stay at Art of Animation, I would recommend getting a car. There are a lot of guests at this resort, and the buses can get quite congested. You may find yourself having to stand for a long bus ride, and that can be tricky with three year old children. Also, having a car is convenient if you plan to dine at restaurants that are located in other resorts. You can simply drive to the resort and park for free, rather than having to rely on bus transportation.
Hope this helps. Have a magical vacation!