Have you thought of using priceline? We've done it twice and been able to get the Westin St. Francis which is right in Union Square. Both times we've gotten it for well below $100 a night.

The last time I was in SF, I stayed at the Vitale, and could not have been happier with both the location and the hotel. The area (the Embarcadero) was great - right across from the Ferry Building which had lots of dining options. It was also an easy to walk to Union Square for shopping and such.
The hotel itself was amazing - there was a wine reception (I believe only once/week) and they even offered complimentary seated massages. My husband and I also spent every evening on one of their rooftop patios facing the Bay. It can be pricey, but shopping around, I have found it for as low as $201/night, and well worth every penny.
Have fun!