Walk around the Cove and the Children's Pool to view the seals and sea lions. There are also tidepools in the ares, but I haven't found them to be as good as many other tidepools. - La Jolla
Go to the Scripps/Stephen Birch Aquarium in La Jolla.
Go to Legoland. The Museum of Making Music is a block away, so you may want to add that, but at the age of your kids, legoland can easily be an all day thing. - Carlsbad
San Diego Zoo. - close to downtown San Diego.
You could spend a day at the waterfront in San Diego. The Midway is there. There's a kitchy shopping area called Seaport Village. You can also catch a ride on the Duck Tour (bus that goes into the bay) or a horse drawn carriage from there.