When you say the Village do you mean West (as in west of 6th), Greenwich (around NYU, Wash Sq Park), or East (east of Bowery)?
Clinton St Baking Company - long lines, arrive early
Blue Ribbon Bakery - long lines, arrive early
Prune- long lines, arrive early
Shopsin's- long lines, arrive early
Best Breakfast and Brunch in Manhattan
113 MacDougal St, New York, NY 10012
Blue Ribbon Bakery
33 Bedford St, New York, NY 10014
Shopsin's is not for everyone (see above), but it is indeed intriguing. You'll have to wait on a Saturday morning, possibly for quite a while. The menu is vast, and the breakfast dishes have a plethora of fans - hence the wait. I've eaten there twice and liked it, although I don't get up early enough to eat breakfast there. Search this board for opinions both pro and con.
I Like Killing Flies is a terrific movie, and it pretty much tells you everything you need to know. Like the flick? You'll probably like the restaurant.