5th Avenue in the Gaslamp
The first time I ever stayed overnight in San Diego was at the "Hotel St. James" which is actually a Ramada Inn. The roof of the hotel is a patio open to hotel guests, and it has an incredible view of the city. If I was a bit more of a risk taker I would take a crack at getting up there, it wouldn't be hard to stand by the door and wait for a guest with a key to come by and let me in, but I tend to err on the side of not causing trouble.
I really wish San Diego had some higher vantage point shooting locations that are accessible to the public.