Depends on what your child is interested in - these are things we've done over the years with our kids when we go visit my parents in SD:
Balboa Park - Zoo (of course), Natural History museum, Model train museum, Reuben H Fleet science center,
Birch aquarium/La Jolla Shores beach/Scripps tidepools/La Jolla Cove (cave kayak tour is fun but your kid might be too young)
Cabrillo National Monument (can get a Jr Ranger badge there) & tidepools at Sunset Cliffs
USS Midway/Star of India/Embarcadero
Old Town - the rock shop, candy store & Whaley House (supposed to be haunted) - these are all things I did as a kid growing up in SD
Carlsbad flower fields (if something is going on there)
Botanic garden in Encinitas
http://www.sdbgarden.org/