R.S.
Hi J.,
I lived in San Diego for 5 years before moving to AZ and still go back frequently to visit. In addition to Sea World, you must take your kids to the World Famous San Diego Zoo! Nearby is Balboa Park which is a great place to walk around with the kids. Near the harbor downtown is Seaport Village (shopping and restaurants) and USS Midway which our boys may be interested in touring with the navy ships. Head over to Coronado is you can either by ferry or car, its beautiful! Now as for restaurant recommendations:
Anthony's Fish Grotto (Downtown on Harbor)
Point Loma Seafoods (Point Loma, near your hotel-great fish tacos!)
Hash House A Go Go (Downtown, 5th Ave)
Miguel's Cantina (Point Loma, near your hotel-great Mexican food, the best cheese sauce for your chips!)
Old Spaghetti Factory (Downtown)
Old Town is right near your hotel as well, they have a bunch of Mexican restaurants, shopping.
Hopefully this helps, have a great time!