Stumptown Coffee Roasters, Greenwich Village, Manhattan
Update - it appears this location has closed
Stumptown Coffee Roasters is a Portland, Oregon based company. They started in 1999 at the beginning of the third wave coffee movement. They now have locations across the US and are one of the few coffee chains that I trust for my coffee tastes. They have 2 locations in New York City. I do like their coffee. However, it can be rather difficult to find a seat in this cafe. Also, you may find that a number of cafes use their coffee beans.
Stumptown Coffee Roasters - 30 West 8th Street between Fifth and Sixth Avenues