I don't think I would recommend Sci-Fi for a 4-year old. He's not old enough to get the kitsch factor, but he is young enough to get scared by the monsters on-screen. Also, not sure if 50's Prime Time theme would be lost on him or not.
I second the recs for either Chef Mickey's (at Contemporary, and easy to get to from Magic Kingdom) or Tusker House (breakfast or lunch) at Animal Kingdom for the Fab 5 characters.
Garden Grill at Epcot has Chip and Dale, Mickey, and Pluto (in farmer outfits) in a rotating restaurant that overlooks part of the Land ride.
Playhouse Disney at Hollywood studios has either breakfast or lunch with various Playhouse Disney characters. (Last I could find on All-Ears was Handy Manny, Oso, June, and Leo, but don't know if that's a current
list.)
Crystal Palace has Pooh characters for breakfast and lunch.
O'hana is fun for dinner, with fun games as PP mentioned.
Coral Reef in Epcot has varying reviews for its food, but one wall of the restaurant looks onto the giant Epcot aquarium.
Biergarten in Germany at Epcot has musicians who play and invite the kids down to dance. The restaurant looks like you're outside in a beer garden -- very pretty.