Hi Sherry! What a great question to have the opportunity to answer. Would you believe at one time there was an actual villian dinner at the Grand Floridian? Sadly those days are long gone, but there are many other great pirate/prince places.
When I was doing some brainstorming over this, I realized my suggestions tend to be more about the special quality if the restaurant rather than the food - I hope that's okay.
At the Magic Kingdom, I do think eating dinner at the Cinderella's Royal Table is great (no princesses! just the Fairy Godmother). It is surprisingly not feminine and has a slightly medieval feel to it. Young princes also get a little sword with dinner.
At Disney's Hollywood Studios, both the Sci Fi Drive in and 50s Prime Time Cafe have incredible theming with the idea of watching something while eating - either a "drive in" movie or old tv clips from the 50s.
If your sons are sports fans, the ESPN Club at the Boardwalk would give them plenty of chances to immerse themselves into the world of sport broadcasts.
At Epcot, the Coral Reef restaurant allows guests to sit alongside a gigantic fish tank and watch all the activity within.
The Wilderness Lodge has the Whispering Canyon Cafe where the cast members are an absolute hoot as they have a few surprises up their sleeves to keep guests laughing and kids active.
Finally, at Downtown Disney T-Rex is being built (not sure of an opening date). We've been to the one in Kansas City, and our sons ask to go back all the time. It is much like the Rainforest Cafe, but all dinosaurs. So much fun!