Mr A's would be a great, but quite pricey, choice.
Does Il Fornaio on Coronado have bay views? If so, that place is yummy. Clay's at The La Jolla Hotel has good food and an incredible view.
Out of all the restaurants in San Diego, Po Pazzo in Little Italy would be my pick. They have amazing food, great ambiance, and an impressive wine list- but no view.
Maybe watch the sunset by the Children's Pool in La Jolla Cove or in Seaport Village, then go to dinner?
Unfortunately, most of the restaurants that are right on the water don't have very good food. If money is no object though and you really want a water view, I'd suggest Bertrand at Mr. A's, the Sky Room at La Valencia, 1500 Ocean at the Hotel Del Coronado, or the Marine Room. If you're ok with something sligntly more casual, a lot of people like Island Prime, which is a steakhouse on the water on Harbor Island. If you can forego the water view - you could also try Oceanaire Seafood Room, Blanca in Solana Beach or Addison, in Del Mar.
re: Alice Q
What about George's California Modern? They're right on the cove and have great food. Similarly there's Tapenade, but the views aren't quite as nice there.
For pure water view and good (but not great) food, Marine Room might be the best choice. Especially at high tide or sunset.