We stayed at the Hilton on the water and it was very child friendly including the restaurants. Lots of local shopping within walking or trolley distance. In the evenings, the family can take bicycle cabs. These are a cheap way to see the area for a reasonable price - esp on a beautiful night!
New San Diego Town Center is the modern city center where boutique shops line the sculptured waterfront. Children can enjoy a stroll along the waterfront, where they can see aircraft carriers and cruises. The USS Midway is parked next to the boat harbor, and you can see many airplanes parked right on the carrier.
http://www.terragalleria.com/california/california.san-diego-harbor.html