Maybe you never heard of third wave coffee. If not, and you like coffee, you should have. The term refers to the artisanal roasters and importers who are as far beyond Starbucks as Starbucks was beyond Folger's Choice. (Hence the term.) New York is blessed with a number of outlets; these are the best ones to get your beans at.
Stumptown is the the Tiffany of third-wave coffee roasters: the best known, the most prestigious, and (arguably) the best. Their cafe and store at the Ace Hotel is certainly the coolest.
As gourmet stores go, Dean & DeLuca is one of the best; they practically invented the form. The meat, produce, and coffee selections are superb, but the cheese case is the star.
Mix third wave coffee with East Village attitude, and you have Ninth Street Espresso, a stark, stripped-down, and somewhat hostile place to drink strong, good espresso. Personally I find their roast to be too dark. But whatever.
No Brooklyn cafe has a more rabid partisan following that Grumpy, whose Stumptown beans and exacting brewing set the standard for Brooklyn baristas.
It doesn't have the name recognition of a Stumptown, but Irving Farm is as good a third wave coffee roaster as anybody -- and is a NYC original into the bargain.
The model of a third-wave cafe, this place is big and airy and makes nothing but great coffee and espresso -- although there is a world-class almond croissant available if you need something to go with your macchiato.
The craft, science, and fetish that is third wave espresso finds no higher expression than at this outpost of the Bay Area original. The place looks like a mad science lab, but the coffee is truly superb.
The coffee plantations of Rwanda produce some of the best coffee in the world, and Bourbon Coffee is devoted to bringing it here. "Bourbon" refers to the coffee varietal, not the whiskey.