Lots of nice hotels in the Bay Area but they can be pricey! I suggest you use one of the many travel sites on the web, look them over, find one you like @ a good price ( under $150 a night in a nice hotel in the City is a good price!) And book it!
You may want to read the forum here about the upcoming October AU Gathering in the Bay Area, lits of Hotels mentioned! Also members Old Trip Reports on here discuss Hotels in the Bay Area!!
I like Kayak and booking.com but there are many including Priceline, Hotwire, Orbitz etc. etc.