Hi Tracy,
Yes, I've arranged and participated in trips to Walt Disney World that included both my parents and my in-laws. We had an amazing time! I think multi-generational trips to Walt Disney World are the best. My son is so lucky to have had the chance to experience the magic with his grandparents.
If you are looking to book three separate rooms, any of the Walt Disney World resorts can accommodate your party. The one you choose will depend upon a number of factors including your budget and the theme parks to which you'd like to be the closest. For instance, you mention Disney's Animal Kingdom Lodge. That would be an incredible place to stay if your boys love animals and you wish to be close to Disney's Animal Kingdom theme park. At this resort, you could either choose three separate rooms or one two-bedroom villa. The advantage of the villa is that it includes a full kitchen and private laundry facilities. You would still have three separate sleeping areas. By comparison, the advantage of three separate rooms is that it affords everyone a bit more privacy and the option to select different (or no) dining plans based on each room's preference.
Another option worth considering, in my opinion, is
Disney's Wilderness Lodge. This gorgeous deluxe resort is just minutes away from the Magic Kingdom and the rustic decor is a perfect fit for active little boys. Check out my article on the Orbitz travel blog on this resort. When you get to www.orbtiz.com/blog, just search for "Disney World's hidden gem" and the article will appear. I bet your family would love this inspirational resort.
Let us know in a follow-up question if you'd like some suggestions in the value and moderate category of resorts too. We'd be happy to help!
Best wishes,
Jill