Hi Laurie!
I am so excited for you guys! I have two boys myself, and Walt Disney World has always been our happy place! We started taking them when they were two years old, and they have grown up with Mickey and Friends:-)
Normally, this would be a tough question because both parks have a lot to offer. However, during your trip, there will actually be a lot of changes going on at Disney's Hollywood Studios, so this would make me suggest that you go to Disney's Animal Kingdom for your third day.
One of our favorite things to do at the Animal Kingdom, that often gets overlooked, is to get there early and go back to the
Conservation Station at Rafiki's Planet Watch. My boys are HUGE animal lovers and you can watch Disney Veterinarians do exams and treatments on some of the theme park animals, and then head out to a petting zoo. It's really one of the highlights of our trip!
There are so many fun things for your boys to do at Animal Kingdom! I know you will have a great time. Please let me know if you have any other questions.