I will second the recommendation for the Holiday Inn. It is also well located to downtown San Diego, the Gas Lamp District, Seaport Village and tons of sightweeing. The Holiday Inn is only 5 minutes from SAN, so any of the hotels in the airport area, Harbor Island or downtown San Diego will work for you.
Check out the San Diego port review located at;
http://www.mexicoportreviews.com/SanDiego.htm
for more information. Enjoy your stay San Diego!
Tom