How interesting! Even before I read the answer, I was about to recommend the Cartwright on Sutter Street! It's one of my favourites, just up from Union Square, and accessable to everything you would want as a tourist!
http://www.cartwrighthotel.com/
Much pricier is the St Francis, which is smack on Union Square, but its historical value is fascinating...they even still wash the coin change they provide guests...(from a long old tradition so as not to dirty the white gloves of 'ladies.'
The other 'boutique' hotel I enjoy is the Orchard, located on Bush street. Same family of owners. It's lovely and the staff are so accommodating.
http://www.theorchardhotel.com/index.php
If you're not a boutique hotel fan, then you can get gobbled up in all the Hyatts, Marriotts and Hiltons in the city. But for experiencing part of the rennovation of San Francisco, you can't do better than these two!
Bon Voyage!
Fr. Bill
www.projectnewlife.org