Sofitel San Francisco Bay
I really like the Sofitel and have also had good experiences there.
Weekends are cheaper - it's a business / conference hotel after all. You can also find it on Hotwire if you look carefully.
I booked 2 nights as a platinum, was upgraded to a Junior suite and was able to combine with a third Hotwire night - still in the suite.
There's not much in the area, but the views are good, and for flyers they will pick you up and deliver you back to SFO free of charge.
Bill