Not inexpensive, but I had the best possible hotel staying experience at this location:

http://www.kimptonhotels.com/hotels/factsheets/argonaut-hotel-fishermans-wharf/index.aspx

The most comfortable fluffy beds, and a staff that bent over backwards to make certain I was 110% happy. One of the few times I've ever felt compelled to write to the company and commend them for good service. I have since stayed at another Kimpton hotel in another city and had a similar experience.

There are other Kimpton properties in the SF area:

http://www.kimptonhotels.com/hotels/hotels-sanfrancisco.aspx