If they are eaters, then Biergarten is an awesome choice. Also, at Disney Springs D-Luxe Burger is sure to please any boys who like hamburgers, though it's counter service and not really themed (it's really good though!).
Satu'li Canteen is the new counter service at Pandora, but the food is a cut above. It's more like the Be Our Guest lunch in that you get real plates and utensils and there is a self-serve soda-fountain with free refills, so that can make it worth it. Boys are sure to dig the "Cheeseburger Pods" which are bao buns with what is essentially a McDonald's cheeseburger stuffed inside (a bit better quality though). They are delicious!
Other's have been mentioned for the theming, like Sci-Fi and Coral Reef, and those are both pretty good. There is also a Rainforest Cafe right at the front of AK (in addition to the one at Disney Springs), so you may consider that in your plans as well. I agree that the food there and at T-Rex is nothing special, but it's decent enough. The kids will like the theming at either.