It seems almost everyone knows Cupcake Cafe but the Cafe side of their shops is often overlooked. They use the superb Marzocco espresso machines with La Colombe coffee. Aside from the drinks themselves, their cafe at 545 Ninth Avenue, all but next to the OTB at 40th Street, harks back to an almost vanished breed of informally eclectic cafes that used to be the mainstay of Greenwich Village. I know of few places left that have this character and feature artisanal quality. However if you are looking for a place with machine like efficiency and the clean lines of a post modern gallery there are plenty of other choices.
Of a more domestic interest is the local chain of Oren's Daily Roast. With a nearly 20 year history in Manhattan, Oren's coffee locations are often neighborhood standbys though rarely raved about. Lately their coffee has taken a surprisingly sharp turn for the better. Of special note are the beans to brew oneself. I have been working my way through his menu and found one outstanding roast after another, absolutely extraordinary. I have gone to great lengths to find outstanding coffee ordering fresh roasted beans from most of the respected roasters in the US and Canada. Many are outstanding providing carefully selected crops, well roasted and delivered to my door. However, Oren's has been so good lately that I can support a local roaster with no regrets. Lately his Kenyans and Sumatra have been particularly noteworthy. An often unspoken secret of great coffee is that if the beans have been harvested recently (within 6 months or so of roasting), roasted carefully, and used promptly and generously, with slightly less than boiling water, it is almost impossible not to have a great cup of coffee all the time - just don't skimp on any of the elements.
One last recommendation: the Van Leeuwen ice cream trucks are now featuring outstanding espresso drinks, or maybe it was the excellence of the barista that day. Nevertheless, the trucks are equipped with a customized version of the Marzocco espresso machine called a Mirage and brew the excellent Black Cat espresso blend from Chicago's Intellegentsia Coffee. I could not have enjoyed my drinks more on a cold Saturday morning at their location in Central Park's revised Tavern on the Green.
Van Leeuwen Artisan Ice Cream
Oren's Daily Roast