Sweet cafe near Penn Station
It's not a cafe, but if you find that you'd like a good burger or sandwich, Stout on 33rd between 6th and 7th is a very nice place to sit down for a nice meal in the immediate area. It's pretty slim pickins around there.
Otherwise I'd wander over to 9th Ave and stroll north of 34th and see if anything tickles your fancy. The Cupcake Cafe just moved a couple blocks down from its original location to 9th Ave and 40th St.
Failing that wander over to 32nd St between 5th and 6th and try one of the many and good Korean restaurants in Koreatown. I like Kum Gang San for more of a sit down experience, but Woorijip is wonderfully chaotic and has a cafeteria/buffet atmosphere with available seating. It's mostly Korean fast food, but it's really good and a bit weird and wonderful. In the back of the place is a window for ordering their delicious (and cheap) noodle soups. Be prepared to find spam and/or hot dogs in your soup, though, apparently they are considered something of a delicacy in Korea.