Anywhere along the coast is good.
Go to the ferry landing on Coronado to shoot downtown San Diego's skyline.
If you go to Cabrillio National Monument (where the lighthouse is), be prepared for crowds.
The Maritime Museum, along the Embarcadero, is always good for photos.
If you have some time, take a few hours for a trip out to
Desert View Tower. It's a mild haul, but you won't find a better view of the desert anywhere.
If you can get up to the Torrey Pines Gliderport, you'll see people hang gliding off the cliffs if the wind is right.
Balboa Park is pretty much a "must see", as well, and there's not a cab driver in San Diego County who doesn't know where it is.
The list of photo ops in San Diego is really pretty endless...