The best bike fitters and service (custom, some stock)
Signature Cycles - Manhattan
www.signaturecycles.com

Has a really excellent bike fitter and great service (custom and stock):
Cycle Craft -Parsipanny, NJ
http://cyclecraft.com/map.cfm?StoreID=1

Friends have purchased stock bikes here and have been really happy with their fit and service. (custom and stock) See their bike fitter Zoltan.
Sid's Bikes - Manhattan
http://sidsbikes.com/

I've heard they are really good with fit and great selection and service. (custom and stock)
Piermont Bike - Piermont, NY
http://www.piermontbike.com/