Try this one - my wife and I have stayed there (we live in Albany, NY) on 4 different occasions, twice prior to a 10 day Mex Riv cruise. It's not cheap, but it is very convenient to ALL of the attractions. There is a car rental facility close by, public transportation (including the trolley which gives you a very comprehensive short trip around town), a great area to walk around and shuttle services (the airport and cruise terminals are VERY close). I think you would enjoy it - the restaurants in the hotel are nice too. There are also nice tours you can take. If you have time, go to the wild animal park, about 25 or 30 miles north of the city (of course, you need a car for this) - this is a little different than the zoo, but both are excellent.
It is interesting, the airport is right in the middle of the city there.
Sheraton San Diego Hotel and Marina
1380 Harbor Island Drive San Diego, California 92101 United States
Phone (619) 291-2900 Fax (619) 692-2337
Enjoy, let us know how it goes. JLK