Hi, Fairy Godfriend!
I'm a native San Diegan myself (still living here, as a matter of fact), and I agree with all the suggestions others have given you for places to see while you're down here. I thought I'd add a couple of suggestions as well. There's an area in San Diego called Old Town, which is very quaint, as well as historic, as it is where San Diego began. It has a Spanish flair, and full of very colorful shops, museums, and some wonderful Mexican restaurants. If you and your son enjoy Mexican food, and make a trip to Old Town, I'd suggest you go to the Casa Bandini restaurant, which is in the heart of Old Town inside a historic building. Beautiful outdoor dining area and the margaritas are to die for! (if you're into that sort of thing, of course, lol) It's a good day trip and located in the Mission Valley area of San Diego, off highway 8 (Taylor Street exit). There's also a Sea World in San Diego, in the Mission Bay area- I can't recall if someone else has mentioned this or not. Also, in downtown San Diego, off Pacific Coast highway, there's another nice shopping/restaurant area called Seaport Village and it's right on the bay. It's gorgeous to go down there and eat near the water and then take a stroll along the boardwalk. If you go over the bridge to Coronado Island, be sure to visit the Hotel Del Coronado- very beautiful and a landmark here. If you have a day to kill and want to see a bit of everything famous here with tourists and locals, I'd suggest going on the Old Town Trolley tour. You pay a fee, should be under $20 a person, and you ride these red, motor-driven, trolley cars that will take you on a tour of several spots in San Diego, such as the Zoo, Balboa Park (stops in front of the famous Aerospace Museum), Coronado Island (stops by the Hotel Del Coronado), Old Town, Seaport Village and a few other places downtown as well. You can get on and off at any of these stops all day, and stay to see whichever places you're most interested in, then catch another trolley to leave and continue on your tour. The drivers are great and give a lot of interesting facts about San Diego along the way. I've taken several friends and family from out of town on these tours, and they've always enjoyed them. You can buy your ticket and catch the trolley tour at any of these stops I've mentioned. I've usually begun at the Old Town stop.
As for hotels, all the hotels suggested are great places. I've stayed at the Marriott Hotel, San Diego at the Embacadero (adjacent to SeaPort Village) and it's gorgeous with a beautiful pool area. Although, it's a bit pricey. There's also an Embassy Suites hotel downtown off Pacific Coast Highway near Seaport Village that's also lovely and has a beautiful indoor atrium. Enjoy your trip! San Diego is a beautiful town (though I am a bit biased, lol).
Amy