Hi Wendy,
You're not too far from the Renaissance Resort once you leave Discovery Cove, and thier Atlantis restaurant is exceptionally nice. It has a more 'adult' feel to it, but the food is supurb. You can't go wrong there.
That said, Planet Hollywood or Rainforest Cafe at Downtown Disney are terrific 12 year old boy options, or perhaps Medieval Times if you are looking for a dinner show.
Pirates is good fun if you're 12 (the food isn't fabulous, but you get to eat in a big room with a pirate ship, which isn't something you can do every day).
Anything on Disney property (maybe Boma at Animal Kingdom Lodge) is going to be good, with the added benefit of the possiblity (not guaranteed, mind you!) of some extra 'magic' coming your way. Ohana is another great choice for a near-teen.
If you have free entry to SeaWorld with your Discovery Cove day, Sharks Underwater Grill is the perfect choice. Excellent food, a jaw-dropping view of the sharks (one entire wall is plexiglass, for a view into the shark tank), and terrific desserts to rival any birthday cake. That would be my first choice, but make reservations ahead!
Whatever you choose, Enjoy! And happy birthday to your dear son.
