I mostly know the East Bay, we came up with some good shops here:
http://forums.teamestrogen.com/showthread.php?t=17093
and here
http://forums.teamestrogen.com/showthread.php?t=22604
Also if you're looking for women owned and or staffed shop check Alameda Bikes and Left Coast Cycles. But any of these would be good. IMHO I'd rather buy a bike that fits at a great shop than shop based on make/model. Trek makes some great bikes but why limit yourself? Lot's of good shops that have other bikes too.
Robinson Wheelworks mentioned in above posts mostly has road bikes (Seven, Mondonico, Torelli, Calfee, Habanero), some high-end mountain bikes but he also has Surly & Riv.
Chris and Steve are not women but I have nominated them for honorary women status and all the perks entitled to thereof because they treat women riders well!!!