billyjack2009 said:
Trolley over the Coronado Island bridge. Lunch at the Del.
While they really don't get into the water, our girls really like doing a beach day at the Del. Looking for sand dollars, building castles, etc. Hotel rooms are run down, food is overpriced, but the beach is nice and they love getting a scoop of ice cream. You can pay for lounge chairs or cabanas.
I second La Jolla. Scripps aquarium is awesome and has an amazing view of the ocean from the outdoor kids touch area. Drive over to the shopping area and eat lunch at one of the casual restaurants with a good view like Cove House before walking down to Ellen Browning Park to see the sea lions. You can walk back up to Prospect to window shop up and down the street. If you're a golf guy, making a reservation at The Grill at Torrey Pines is a great experience and amazing view of the ocean and course.
The zoo is iconic, but our kids like the wild animal park better. I think they renamed it to Safari Park and is like Disney World's Animal Kingdom. It's just a bit of a drive.
If you do the zoo, make time to check out the train and carousel. Your kids are getting older, but I bet they still like it. The carousel is one of the oldest left if I remember correctly. Then walk over to Balboa Park and walk down El Prado to check all the cool stuff like the botanical gardens, fountains, lily ponds, and other museums, etc. It's not cheap, but lunch out on the terrace at Prado is pretty nice.
My wife's family all lives in San Diego so we go out at least once a year to visit. Let me know if you have any questions. My girls are currently 5 and 9.