i have good things to say about almost all of the NYC shops I've been to.

as someone else said, different places specialize in different services / inventories. my #1 choice for mechanic work is Bike Works in the Lower East Side. Now that I live in Brooklyn, I trust B's Bikes in Greenpoint to do easy-to-medium mechanic jobs for cheap. Other than that, it just depends on what I need.

Even though I'm a mechanic myself and a Time's Up member (meaning I have a whole shop of tools to use when I need them and access to a wholesale bike parts account) I try to patronize local bike shops whenever possible. It's important to support the local cycling economy and I know these guys are on the front lines of promoting cycling throughout the city.