The problem with smaller coffee shops (especially in NYC) is that they open-up, close, or worse yet change quite often.

Good coffee is based on the Barista. The best environment depends on your purpose and tastes. These 2 things will contribute to the best answer for this question and are subjective.

I would check out this site:
http://www.cupofnyc.com/
It has user submitted reviews and ratings of local NY coffee shops.

New York Magazine also talked with several foodies to try to find a similar answer:
http://nymag.com/urban/guides/bestofny/food/04/coffee.htm

The last time I was in New York, I was taken to this place:
http://www.moccalounge.com/
I noted it in my blackberry at the time as a place I would like to visit again.

I sincerely hope that this helps Easyeboy!
Source(s):
I'm sorry, I didn't use the search engines you suggested but did do an extensive Google search to discover up-to-date user submitted reviews for your consideration. I also have spent a little bit of time in NY on business and share your affinity for good coffee.

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You have the good fortune to be in one of the best coffee cities in the world. NYC is a leader in what's being called (perhaps pretentiously) the "third wave" of the coffee renaissance:

http://www.baristamagazine.com/Issues/VolumeII/AprilMay06/aprilmay06-third.html

This New York Times article has a great rundown on the key places:

http://www.nytimes.com/2008/10/26/nyregion/thecity/26coff.html?pagewanted=all

Of particular note is Cafe Grumpy in Chelsea, who get their coffee from Intelligentsia:

Cafe Grumpy
224 W 20th St, New York, NY 10011 (between 7th Ave & 8th Ave)
212-255-5511
http://www.cafegrumpy.com/

Here in LA we have Intelligentsia (from Chicago) and LA Mill which are great, but there's little else in the "third wave" category.
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This place http://www.portorico.com/store/ is located downtown and makes very strong stuff. They have a few locations http://portorico.com/store/page68.html. I'm not a coffee expert so I won't critique their product, but friends have spoken very highly of it.
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I tried a bunch of them, looking specifically for Caffe Reggio. After the 5th one, I got to it:

http://www.menupages.com/restaurants.asp?headersearch=yes&txtHeaderSearch=caffe+reggio

I also tried foodle.net, opentable.com, dinesite.com, and fastnosh.com without success.
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