In your post, you referred to the Sci-Fi Dine-In Theater at Disney's Hollywood Studios. Guests sit in cars, as the experience simulates an old-fashioned drive-through movie theater. Most reviews around here complain about mediocre food, but every Disney fan should try the place at least once! The same goes for the 50's Prime Time Cafe, located in the same park. There, you will sit in a miniature recreation of a stereotypical 1950's American kitchen, eat traditional comfort food and deal with playful servers acting like a sitcom mother. Your children will likely enjoy both places.
Have you considered any character meals? All four parks offer them, and you should choose one based on the characters your boys like the most. Do they just love Mickey and the gang? I recommend Donald's Safari Breakfast at Tusker House in the Animal Kingdom. Pooh fans? Try Crystal Palace at the end of Main Street in the Magic Kingdom.
I also suggest considering Coral Reef in Epcot. The restaurant features a gigantic aquarium, and every table boasts a wonderful view of the marine life while you eat.
Hope this helps a bit!