What part of the Bay Area are you headed to? If San Francisco, unfortunately there aren't any shops that specialize in reef tanks. If you can head to the East Bay (Oakland) and South Bay (San Jose) then you can go to these shops as you travel down south on Highway 880:
1. Aquatic Collection - Hayward
2. California Reef Co. - Fremont
3. Neptune Aquatics - San Jose
Once you touch down in Oakland it'll take approximately 1 hour to drive south to San Jose to Neptune, then you can head back up north, stopping at each shop. Fortunately they're all close to the freeway. All are worth a visit: they are all clean, well-run establishments with a nice selection of SPS, LPS, and fish. If you're into anemones, Aquatic Collection has been getting some nice ones lately.
There are other shops around the Bay Area, but unfortunately they are too isolated to be worth a visit. However, if you tell us where you're working and staying, we can help you plan accordingly.