While your kids will love the proximity to SeaWorld [1], you’ll love the almost European stylings of the classic ocean-side resorts on Point Loma and Shelter Island. You’re still within easy driving range of all major San Diego [2] attractions, without the crowds and the downtown feel.<
If you own your own boat and plan to bring it to San Diego, consider one of the resorts on Shelter Island—most have private marinas that rent slips.
Links:
[1] http://www.moon.com/destinations/california/san-diego/sights/mission-bay/seaworld-san-diego
[2] http://www.moon.com/destinations/california/san-diego