Moonbass, I had some peculiar problems with a bass and looked around for someone to help. I went to two of the bigger names (Rudy's, Matt Umanov) and wasn't too happy with the results (note, this was a fairly strange problem, or couple problems; I'm sure either place could do a regular setup without hassle, although they probably get good money for it).
The best guy I've found is Gary at:
friedguitars.com
-this guy really helped me out in a jam and didn't even want to take my money. He's in Brooklyn, a quick ride out to the Atlantic-Pacific stop and two blocks from there.
Before I found Gary, Rick Turner recommended Flip Scipio to me; Flip was unavailable and recommended Norio Imai. I haven't met or worked with either, but I think you could find both through google.
If you try a search on Talkbass you'll get a lot of options as well.