Hi Jennifer! I also have two boys, ages 8 and 11. We often base our resort choices on transportation to parks as well.
Obviously, the Contemporary and Wilderness Lodge will be most convenient to Magic Kingdom Park. You can be there with a quick trip on the monorail or by ferry. All parks will be available by bus from Animal Kingdom lodge. The bus rides are fairly direct, with few to zero stops, so although the lodge is a bit farther away, the bus ride is not that much longer than from other resorts that make multiple stops.
With two boys, I think Wilderness Lodge and Animal Kingdom are both awesome choices. The rustic, camping feel of Wilderness Lodge is always a favorite of ours, and Animal Kingdom offers savannah view rooms that can mean waking up to a giraffe at your door! I think all children would love that! And all three of your choices offer great pools and play areas.
Here is a link to an overall view of
transportation options at the Disney World Resort area. I think you should sit down with your family and choose the resort that looks the best to you. I really don't think transportation will be a huge plus or minus at either of the three resorts you like. It's always a good idea to allow at least 45 minutes of travel time no matter where you plan to start and end at. And really, riding on the different modes of transportation, (monorail, boats, ferries, buses) is all part of the fun at Disney World!!