S.B.
Yes - second the Legoland. It's in Carlsbad, which is still San Diego metro area, even though that's hard to make out map-wise.
Coronado Island is very, very pretty. Go visit the Hotel Del Coronado (Or if you're so inclined to pay through the nose, staying there is unbelievable).
Seaport Village is a neat little collection of shops downtown / on the bay. Worth an hour or two of idle time & watching the boat activity.
As for beaches...Pacific Beach is the one that "looks" like a little fun beachy place. Old time roller coaster, boardwalk, etc. The other beaches are fine, too. For kids, I personally prefer to do Coronado Island beaches - little less of the teenage/college/party crowd, but then again, that's part of the atmosphere of the beach, too.
Downtown - Gaslamp District is neat - and the mall - Horton Plaza - is pretty cool.
Old Town is neat to see. Exactly what it sounds like - an old town - tourist area.
You're already going to the zoo, so you'll be in Balboa Park - it's very beautiful - all the museums, etc. Always a festival of some sort happening somewhere around there. Adjacent to that is the community/town of Hillcrest - it is predominantly considered the "gay" district, but oh, so much fun - neat shops, all walkable.
Oh, I miss San Diego! You'll never want to leave - it's just beautiful. Have a great time!!!