We stayed at the Omni San Diego last fall and absolutely loved it. I would wholeheartedly recommend it to anyone. Are you worried about the trolley noise? I really didn't notice that at all. If you are on the bay side, you might hear horns from ships from time to time, but nothing that is going to keep you up at night - I am a pretty light sleeper and it didn't bother me at all.
We have also stayed at the Hotel Del Coronado, which is a great location (right on the beach). The newer buildings are amazing, but not cheap. Check it out, it might work for you.
Good luck!