Coral Reef with the aquarium is very nice. I agree Sci Fi is also fun, most kids enjoy sitting in a car under the stars to eat their burger! O'Hana for dinner doesnt' have characters but has coconut races and other stuff for kids to participate in and some very nice views of the castle if you get near a window.
If he is in to Dinosaurs, T Rex Cafe in DTD might be a hit as would Rainforest Cafe. Altough they both have darkness, animatronics and at RFC they have these thunderstorms that produce thunder, all of which might be too much depending on your son. I know at 3 my now 14 year old son couldn't have handled that, my daughter would have loved it!