Manhattan:
Porto Rico Coffee- They're all over the place. The 'fresh' beans in burlap sacks look appealing -- there's a variety of roasts and beans. Unfortunately, they're almost always old and stale. Few know how long they've sat in the store, or how long in the warehouse before- especially not the employees. They're also not roasted by an artisan, its just a family commodity business -- not as much love or understanding of the beans that you'd like. That said, they're great drip coffee for the office. Far better than Dunkin Donuts or Starbucks, and on par with the whole foods site-roasted stuff. The Yirgacheffe they have is always great, and a few of the blends make a great 'truck stop' cup. It's roasted in the Burg, and you can get fresher beans directly from their roaster if you call up. They also do a fresher delivery service to many cafes. The espresso blends are charcoal and taste like shit, they pull with no crema. A drink in store is on par with one at starbucks -- ie, not worth your money.

Trader Joes- Some people swear its great- I swear they're idiots. TJ coffee is nitrogen flushed and months ( if not years ) old by the time you get it. Buy their Kona if you want a good example of how to ruin a bean.

Whole Foods Market- While they boast the fact that they roast on premises, its just a regular employee putting beans in a fluid bed roaster for a pre-determined time. There's no knowledge or love going into those beans. And they're crazy overpriced.

Dean & Deluca- Overpriced and stale.

Dunkin Donuts- Honestly, they really are the best cup of basic coffee you can get from a chain in NYC. Half the price of starbucks, and three times the quality.

Starbucks- Their mermaid should be canonized as the patron saint of the Tasteless, Ignorant, and Trendwhores. Its really just not good and overpriced. Their espresso is downright disgusting. Instead of replaced poorly trained baristas who make bad espresso with automatic machines that make bad espresso, they should lower the char in their beans and replace all the machines with Moka pots. The only benefit to drinking starbucks is that their regular coffee tends to have more caffeine than other retailers (though it changes on the batch).

Ninth Street Espresso- They have their own blend that is freshly roasted, but I'm not a fan. Its roasted too dark and seems to have a bit too much 'bite' for my taste (spicy hings from indonesian beans?). In milk, its not that bad. Occasionally they'll have a guest blend - those a very good days. The staff is talented and knows how to work the equipment- tons of crema, and beans are always on the right day. I honestly just don't like their blend all that much - other blends come out wonderful. Their blend pulls roughly the same at home on a single boiler and e61 hx as it does in store- its rather forgiving on temp.
Despite my negative words, I put them clearly in the top 5 best coffee shops in NYC.

Joe The Art Of Coffee- To Be Reviewed

Brooklyn

Gorilla Coffee ( park slope ) - The drip is great. The espresso tastes like gorilla shit. I'd avoid it at all costs.

Oslo ( 2 locations, williamsburg ) - Their own espresso blend is roasted at Dallis Coffee (there is a roaster at the original location, but they can't use it because of the lease). I have mixed feelings on their blend. A few times I've had it, its been a bit too spicy-- other times, its been too berry. I've never had it hit 'just right'. Beans seem to be fresh, though the staff is often clueless about it. They're super helpful though, and will actually whip out a cell phone and call the owner to find out the roast date and optimal temps if you ask. Tastes good in milk. Their blend pulls roughly the same at home on a single boiler and e61 hx as it does in store- its rather forgiving on temp. There could be more crema - which means the staff could use some better training. Their house coffee is tasty when black- big on the berries. Regardless, I put them clearly in the top 5 best coffee shops in NYC.

St. Helens Cafe ( williamsburg ) - They have vivace flown in, and pull it on a standard beat up la marz ( i think... its been a while ). They know what they're doing- they have the beans , a reliable machine, and pull it well. I put them in the top 5 best coffee shops in NYC.

Gimme Coffee ( williamsburg ) - Brooklyn storefront for upstate microroaster. Coffee is fucking spectacular. Their Leftist espresso blend tastes like a square of dark chocolate and pat of butter melted in a demitasse. MASSIVE crema. I give them "best espresso in nyc" by a mile. The milk based drinks are pretty top notch too, as are the drip coffees.
On a personal note, i think the leftist and platinum blonde have had too much robusta in them lately- i haven't liked pulling shots at home in recent months. I was once told that the Leftist was predominantly the Mexican Malinal dark roast with some robusta and something else. Malinal beans are great because they're really forgiving on temperature- a bit too high or low, and you're still good ( some beans have a 2°C band of forgiveness, I've ranged 10° off with great results on a malinal ). In any event, if you want to pull on a home machine that doesn't have a PID, i'd suggest going for the Dark Malinal and do single origin shots - I've had better results on that ( though it will come out with massive amounts of Dark Chocolate and Cherries )

Cafe Grumpy ( williamsburg ) - To Be Reviewed (they're getting good reviews now, so I'm willing to take a trek - but some friends who went on the first week had the worst expereince ever as the staff/owners had allegedly never used a machine before and were still being trained )

UPDATE- I've now been to the Cafe Grumpy locations in Chelsea and Greenpoint twice each, so here goes:
The Synesso is fucking amazing. What comes out of it, in terms of temp stability and crema, is unbelievable.
That said, I don't like Grumpy. The beans on each visit have either been too old or too new. Sure -- it would be better if I had beans on day 7 than 4 or 9, but i was in there and served the off days. The baristas that served me were not nearly as talented as the guys at any of the other top cafes -- the Synesso was doing the bulk of the work, and I tasted it. The shots weren't 'bad' -- there was nothing truly wrong with any of them -- there just wan't anything truly 'right'. This happened on more than 1 trip, and at more than 1 location - so , as far as i'm concerned, its endemic to them. I couldn't help but think how much better the shot would taste if someone from gimme or 9th street pulled it. I also couldn't help but think that I might be able to run behind the counter and pull a better shot myself. They sell whatever they're pulling at the time by the pound, but its quite a bit more than ordering it online ( even with overpriced 1lb shipping). In a nutshell, I just didn't get the vibe from them as I get from other shops, and seriously wonder what a synesso could do at the other shops.
That said, I grudungly place both locations in the top10 places in NYC-- not so much on merit , but that they have less things wrong with them than other cafes.

The Verb ( williamsburg )- The drip tastes like a piece of plastic is burning, and the espresso is thin and burnt with no crema. The place is always packed because of location, not quality. Wireless costs $$.

Fabianes ( williamsburg )- The espresso & drip are acceptable, but there's no apparent microroaster quality. I think its all prepackaged beans. Unfortunate.

The Fix ( williamsburg )- The drip is pretty decent. The espresso is not ( thin and made by untrained staff ). I've never seen milk foamed properly. Wireless is free and has a decent speed.

Read ( williamsburg )- The espresso I had was not good. The drip was drinkable.