If you're looking for a shop with a nice looking showroom and can take a test ride then check out Sid's Bikes on either 19th between 6th and 7th Avenues or E34th between 2nd and 3rd; the staff are pretty friendly as well. There are lots of other good shops in the city with better wrenches but they're not that big or are cluttered which is a pet peeve of mine. Here are a few that come to mind:

Sid's Bikes
R&A Cycles
Bicycle Renaissance
Toga Bikes