"We went to San Diego last June with 3 and 5 year old. We did all the standard amusement parks -- Lego Land, Sea World, the Zoo, the wild animal zoo, and the downtown San Diego with the ships and submarines that are there. The kids absolutely loved it. The theme parks tend to get crowded but they are very well equiped for families with children and you can rent a stroller or anything else you need. We arrived right at the opening time which is not hard to do with children who are up at 7 every morning. I believe in traveling light and renting everything once you get there. We drove to La Jolla one day b/c my husband remembered how beautiful it was but frankly the beach outside of our hotel in Coronado was much better for the kids. If you do the Zoo, which I recommend b/c you can't even begin to compare it to the Washington Zoo, renting a stroller is a good idea but you go up and down the hills a lot so pushing a stroller is pretty taxing. There are shuttles that you can take, but sometimes you still have to walk, so I hope your kids are good walkers. My kids actually did great walking everywhere that day, it was the only time we did not rent strollers.
In my opinion, Sea World is the most "commercial" of all the parks but from the child's perspective it's great. We managed to get back to the hotel every day and enjoy the beach and the pool."
California
California
In La Jolla, you can visit Children's Beach to see the seals. I'm not sure what else you would do there with children.
Outside of La Jolla, we had a good time at Sunset Beach, at the Balboa Park Fountain and at the Science Museum in Balboa Park. Your older kids would love the science museum; they have little phone booths, a play grocery store and all kinds of interactive exhibits that are meant to make noise and enjoy. My daughter was fond of drumming along to Jimi Hendrix songs.
The zoo sounded like a nightmare to me. Everyone said we "had" to go, but I have no idea why I would want to pay $90 to see animals in San Diego that I can see here for nothing. It also sounded crowded and like a madhouse, and that is not my idea of a relaxing vacation.