Hi Melissa!
My top two recommendations for boys that young would be Chef Mickey's in the Contemporary Resort and the Crystal Palace in the Magic Kingdom.
Chef Mickey's is a "must do" for my family, and my children are 10 and 5 years old. The last time we were there, we saw Mickey Mouse, Minnie Mouse, Donald Duck, and Goofy. While the characters change from time to time, I think it is safe to say that the Big Cheese himself, Mickey Mouse, will always be there while his name is on the door! It's been my experience that the characters spend a lot of time with each table. Also there's a lot of excitement in the restaurant.
Crystal Palace is a wonderful place to dine in the Magic Kingdom. I think the buffet is great. They offer breakfast, lunch, and dinner there. Most young guests enjoy interacting with Winnie the Pooh, Piglet, Eeyore, and Tigger.
If you can't get a reservation for either, then other options include 'Ohana's Best Friends Breakfast featuring Lilo and Stitch in the Polynesian Resort, Play 'n Dine at Hollywood and Vine in Disney's Hollywood Studios, and a Character Breakfast at Cape May Cafe in the Beach Club Resort.
Some advice when visiting with young children: Slow down and enjoy the experience of visiting with young children instead of running from attraction to attraction; take your own stroller because your children will be familiar with it; consider staying at a monorail resort or renting a car to allow you to return to your hotel quickly to take a nap, rest, etc; don't rush character interactions until you see how your children respond; do those things that your children find most interesting. The most important thing of all is to just have fun!