A lot depends on what type of Deep Sea Fishing experience you are looking for. The 1/2 and 3/4 Day trips mostly fish the local waters and will go after whatever is biting that week. The 1-2 day trips usually are after some type of Tuna (yellowtail, albacore, etc.). The Long Range trips are not for someone who doesn't yet know if they like being at sea or not.
You can have a good time on any of these trips. If this is your son's first time you might want to ask the landing to recommend a less crowded boat or a day when there are less people usually. The weekends can get a little hairy if there is a full boat. There may even be a special "beginners" trip available.
Here are a few links for you to start your research. Also, I would suggest staying one or 2 nights in the area and seeing some of the other sights. Hell, you could go to SeaWorld the day before you go fishing to get a look at what you will be going for.
Fisherman's LandingH&M LandingSan Diego Sport Fishing OnlinePoint Loma SportfishingI just googled these under "San Diego Fishing". There are a lot more sites for you to research. The boat captains know that the people want more fishing time but they also know where the fish are. If they have to run longer to find the fish you will have a better time catching fish in less time than fishing a lot and catching nothing.
After you book your trip try to watch the fish count reports on the websites. This will give you an idea of what is running. Also, if you don't have your own tackle, they all have rentals available. Some are better than others though, so if you don't think what they give you is any good ask if they offer a better grade of rental tackle at a slightly higher price.
Above all Have Fun!!!! And remember to get the non-drowsy sea sickness pills.