The San Diego Zoo is the best thing to do in San Diego with kids because nobody ages out of it. A 3-year-old and a 15-year-old come off the same hillside arguing about different animals, and the place is set up so that tired legs never end the day early. It will take a full day off your hands and hand it back in good condition.
After that it scatters across the county — an aircraft carrier tied up downtown, open savanna in Escondido, a marsh in Chula Vista you can only reach by shuttle, a free beach in La Jolla with showers and a playground, tide pools under the Point Loma cliffs that only exist for a couple of hours at a time. Some of these are a whole day. Some are finished before lunch, which on day four of a visit is exactly the right answer.
Half of them run on a seasonal calendar, so look up your exact date before you promise anything to anybody. Then pick one, do it properly, and let the second one go.
For a broader first-visit plan, use the main San Diego things-to-do ranking; for a day that costs nothing, the zero-admission list; and for a water day, start with the best family beaches before comparing the broader beach ranking. If one of these is turning into a monthly habit, run the household math in the San Diego memberships and annual passes guide before buying another set of tickets.