There is a good cafe just out of Crown Heights called Manhattanville, they are not the cheapest cafe out there, but the coffee and pastries are pretty good. They weren't always under hashgacha, but now only serve cholov yisroel milk and have supervision under Rabbi Aaron D. Mehlman, Executive Rabbinic Director, National Kosher Supervision.
167 Rogers Ave (corner of St. Johns)
Brooklyn, NY 11216