Hi! I have a 10 year old son and he tells me he loves Disney's Animal Kingdom the best, followed closely by Epcot, and then Disney's Hollywood Studios. He also likes the Magic Kingdom, but just not as much as the others. However, he loves thrill rides and he's been to Walt Disney World once or twice a year since he was born.
I, however, recommend visiting the Magic Kingdom first since this is your first time. It is the crown jewel of the Walt Disney World Resort. Most 8 and 9 year old children will enjoy all of the attractions there. My son especially enjoys Space Mountain, Splash Mountain, Big Thunder Mountain Railroad, Buzz Lightyear's Space Ranger Spin, Haunted Mansion, and Pirates of the Caribbean. I also highly recommend watching the Wishes fireworks show from the top end of Main Street -- closer to Cinderella Castle.
At Disney's Animal Kingdom, my son absolutely loves Expedition Everest followed closely by Dinosaur. At Epcot, his favorites are Test Track, Mission Space, and Soarin'. Your boys may also enjoy "The Sum of All Thrills" attraction inside Innoventions at Epcot; It lets guests create their own ride experience. At Disney's Hollywood Studios, my son enjoys the Twilight Zone Tower of Terror and Rock 'n' Roller Coaster.
My son also loves the water parks, especially Typhoon Lagoon. The theming there is incredible. With only 3 days, I would normally suggest you concentrate on the four main theme parks, but you should consider Typhoon Lagoon or Blizzard Beach if your sons love water!
For a Moderate resort , my family loves the Alligator Bayou section of
Port Orleans Riverside. We love the theming there and my children absolutely love the pool area there. If that's unavailable, my next recommendation would be for the Caribbean Beach Resort.
Enjoy planning your vacation and write back if you have any more questions!