Hi Victoria,
Although both Resort hotels that you have mentioned are fantastic places to stay I think that in your situation and given the choice, I would opt for the
Villas at Disney's Wilderness Lodge.
As your children are still very young, I would imagine that you will be spending a fair bit of time at the Magic Kingdom theme park which is located only a short boat or bus ride away.
There are lots of recreational activities available at this Resort for both children and adults alike. You can find out more information about what is on offer
HERE.
The main pool at the Wilderness Lodge Resort is called Silver Creek Springs. It is a lot of fun and even comes complete with a water slide and hot tub. Inside the Villas at Disney's Wilderness Lodge lobby, you will see a spring bubbling
over stones. You can follow the water as it flows under the lobby's window wall,
widens and becomes a creek in the Resort's upper courtyard and then transforms again into a sparkling 15-foot waterfall, which
empties into the main pool.
Don't get me wrong, Disney's Animal Kingdom Villas are great as well but in my opinion, the location is not as convenient as the Villas at Disney's Wilderness Lodge.
I hope that this information has been of help & wish you a magical trip!