If you're far up in Greenpoint and need caffeine + snack, Bakeri is my spot (I say "bake-ery", others say "bach-ery"—I still vote the former). Known for their baked goods—both savory and sweet—it's the perfect spot for a coffee meeting, small breakfast, or a solo book read. There's one large communal table in the center, plus a few two-tops and decent counter space—one of the rare cafes with enough room that it's rarely packed (except saturday!).
Cobble Hill Cinemas is a cozy little neighborhood theatre. It has all the charm Brooklyn has to offer, screening new releases as well as selected independent films.
My second-favorite outdoor-place in Manhattan. The abandoned 1.6 km rail tracks running above Chelsea down to the Meatpacking district were turned into an above-ground park. Perfectly nice place for sitting in the sun, reading, relaxing, having lunch in some green spot in the city. Nice views at the Hudson River, New Jersey, the Statue of Liberty (little small from there but still visible) and the architecture around Chelsea.