Hi Jessica,
While I think all of the moderate resorts are excellent options (each has well-themed pools, immaculate rooms and both table service and food court-style restaurants), my vote is for Caribbean Beach Resort with boys. I recently toured this property, and saw the newly-renovated, pirate-themed rooms. All I can say is "wow"! The attention to detail is amazing, and sure to delight any little pirates-in-training. The beds resemble ships, with bedspreads that look like jewels and other "loot", and the carpet is like a giant treasure map. If your boys like to swim, they should be happy with the nine (yup nine!) pools on property. The main pool area is amazing, and features a pirate splash pool with slides that are the perfect size for your kids, water canons and water falls. The grounds resemble a lush, tropical island, and are very colorful.
Caribbean Beach is an Epcot area resort, (it's located near Epcot, Downtown Disney and Hollywood Studios). Transportation to all of the theme parks is via bus. (This is the case at all of the moderate resorts, by the way). I think you'll find transportation to be convenient and easy.
If you are interested in seeing some detailed pictures of Caribbean Beach or any of the other moderate resorts, you can visit the independent website
www.allears.net, and search accommodations.
Have a wonderful trip!