Living in the East Village, I'm very fortunate to live within walking distance to four great coffee spots: The Bean, Think Coffee, 9th Street Espresso & Joe - The Art of Coffee.
While most of them serve breakfast muffins, pastries, etc....almost all of them serve mediocre chocolate croissants. I'm talking about a real pain au chocolat, like the one you'll find every morning in wonderful Parisian patisseries. What I've been craving is flaky, baked croissant with two bars of chocolate through the center....not the enriched bread, flat-tasting croissants most of the coffee joints in the area serve.
Well, after months of searching, I think I've found a leading contender -- Tarallucci e Vino is a very cute Italian coffee/wine bar. There are two locations, the original located on East Tenth Street and a larger, more swanky location in the Flatiron District (East 18th off of Broadway). They serve wonderful pain au chocolat -- flakey & crusty, yet soft and the chocolate tastes rich and dark. Enjoy one (or two if you are indulging) with a capuccino.
Even better is that you can even still get them in the afternoon (they don't run out of the quickly like a lot of shops).
Tarallucci E Vino
163 First Avenue (10th Street)