J.R.
I would plan on going in maybe July or August if you are wanting to spend alot of time at the beach. The water is still very cold in June and only tolerable in July or August. Also plan on bringing sweatshirts as it gets really cool in the evening, especially if you are on the beach. The Zoo is huge so wear comfortable shoes and don't expect to see it all in one day. La Jolla is beautiful as is Coronado Island. I second the other mom's suggestion about the Hotel Del Coronado and Sea World and LegoLand is close but I haven't been there. We love San Diego!!! Another option for you is Catalina Island (you take a ferry out of Long Beach) and then you would be closer to the attractions in LA (Disney Land, Universal Studios, Hollywood, Beverly Hills etc).