There are a lot of great stores in the area, it really depends on where you will be staying. In the city there is Dottie Doolittle (3680 Sacramento St). Sausalito has Cha Cha Cha (a fabulous store!!!)- (589 Bridgeway). Mill Valley has Kidiniki (301Strawberry Village). Noodle Soup in Corte Madera (117 Corte Madera Town Center- Great Shopping in this outdoor village) and Lullaby Lane in San Bruno (556 San Mateo Ave).
I don't think you could go wrong with any of these stores. They are all wonderful stores and have a great boutique selection with lines like zutano, le top, kissy kissy, rabbit moon, etc.
Hope your trip is super fun!
Kristin D.