Laughing Squid has a recent article about the improving coffee situation in New York. At one point, it seemed that all coffee in NYC was going to be Starbucks or Dunkin' Donuts or even McDonalds, but the advent of the small coffee shop is coming in full swing here.
As a recent Brooklynite, one coffee shop I have become a fan of is Coffee Den near Red Hook. It's a small place, family and friend owned, but they brew one hell of a cup of coffee! I can't imagine a Saturday passing by where I'm not there, having a mug of red eye or hot chocolate while I study. The relaxed atmosphere and local regulars make it a nice place to start a Saturday for me.
There are many other coffee shops like this one, which I love. These are the kinds of places that care about what kind of coffee they serve, the quality of their foods, and friendliness towards customers. It's the sort of coffee shop that's more popular in other parts of the US, but is becoming a big part of Manhattan and Brooklyn.
Read the article about coffee shops via Laughing Squid.