Not a cafe, but the Rose Reading Room at the 42nd St. library is the prettiest, most productive place to get work done. Also easy to move outside to Bryant Park when it's nice out.
The lesser known but very nice alternative is SIBL: Which has nice workspace in its lower level reading room. This is more quiet like a university, and not like a hip/trendy etc. But they also have photocopy, print, and research materials if you should need some.
NYPL: Science, Industry and Business Library (SIBL)
A good choice however you are not allowed to consume your own food/water/coffee there. So if you have something you need to do in two hours or less with no breaks, then this is a great place.
How loud is it there? The stone walls and tile floors make me think it's very live, acoustically speaking. Are people quiet enough that it's not a problem?
There's a lot of love here for the 42nd St. library, but I'm personally a fan of the performing arts library at Lincoln Center. Aeron chairs, tons of open space with plenty of outlets, and if it's warm out you can work in the Lincoln Center plaza for a change of pace.
If it's warm out and you don't need internet access, I'm also a big fan of working from the High Line. There are lots of shaded tables, and you can't beat the ambiance. If you need to duck away for power or WiFi, Chelsea Market has both nearby (although getting a place to sit at Chelsea Market can be tough if it's after 11am or so).
There's tons of places in NYC, but here's a few places I've been known to frequent
- Cafe Amrita, near 110th St and Central Park West. Generally has a pleasant buzz. I've noticed other techie types there, but not tons. They kick out the laptop crowd out on weekends, and at night they become more of a bar.
- Tea Spot, near MacDougal and West 3rd in the Village. A smallish place that has always been pretty quiet when I've worked there. NYU students are most of their customers, I reckon.
- Cosi near 23rd st and 6th Ave, in Chelsea. This is a chain, but this particular Cosi is well-lit, has good internet service, is large, and never seems to be very busy.
- As others have noted, New York Public Libraries are often great places to work. I sometimes sneak off from my office to use the Hudson Park Library, which is near Leroy and 7th ave in the Village. Its a tiny little branch library, but its quiet and the internet service is fast. There's a lot of little branches like that, look on the web site for locations.
The Cosi on 8th between Greene and Mercer by NYU is the same way. Even when I can't get a seat at any of the surrounding coffee shops this place is mostly empty with plenty of outlets and free wifi.
As someone else suggested check out Loosecubes.com .
In Manhattan it can be a little challenging to find a coffee shop to set up in for very long. Seats and outlets are at a premium and many are policing wifi moochers these days. There are a few large starbuckses with a good amount of room though. I've also worked at the library before (not many outlets, and you can't take phone calls inside).
In Williamsburg there are a ton of work-friendly coffee shops. If you take the L train to the bedford, lorimer or graham stops, pop open Yelp and you'll spot at least 3-4 coffee shops in a 5 block radius of each, with wifi and (usually) seats...
The Rose Reading Room is beautiful, but the wooden chairs are a bit uncomfortable if you plan on being there for a few hours.
I suggest the Science, Industry and Business Library (SIBL) on 34th and Madison (http://www.nypl.org/locations/sibl). They have a big room full of about 150 workspaces to work from your notebook with power, Wifi and Aeron chairs. I've been there several times and did not run into any issues with finding an open seat.
Im going to get downvoted for this but whatever: the 24 hour apple store, when you need a clean well-lighted place past midnight. It's close to the yellow line and there's always a food cart outside.
There's seating and the light isn't too harsh for being fluorescent. I've seen people go there without their own computers and basically look as if they're editing video for a project...and the staff pay no mind.
Don't know what they'd say if you planted a dell laptop on one of the unused Genius bat areas, though
While I'm on the topic, the Apple stores in SoHo and in UWS have comfortable theater seating. I've planted myself there and even if you don't have headphones, the Apple Genius giving a walk through of how to use Keynote/iCloud/whatever makes for decent background noise
Different strokes for different folks. I thrive in the noise of the Tea Lounge. I also second the Ace Hotel, which includes a Stumptown for you coffee fiends.
I just moved to Brooklyn a month ago and spent about a week looking for great coffee places to get some work done. I came across this one place called The Tea Lounge on 7th Ave and Union St. I've kept it secret from those around me because I don't want the place anymore crowded than it is, so just keep this between me and you.
If the weather is nice, you can work in Bryant Park during the day. Especially before lunch hour rush. There are tables, shade, and (some) wifi -- though 4G cell hotspot is probably better.
Also, the New York Public Library is right nearby, so if you get annoyed by crowds or weather, you can relocate to one of the most beautiful quiet workplaces in the entire city.
As GMFlash said, Science, Industry and Business Library (SIBL) on 34th and Madison (http://www.nypl.org/locations/sibl). It's very consistent with comfortable chairs for working.
I work out of General Assembly (a co-working space between Union and Madison Squares). You're welcome to work from there for a day as my guest if you like.
I'm assuming you're talking about the Think on Mercer. Just to clarify, the Think on the Bowery is much smaller and has no wifi (and last time I was there had a passive aggressive sign about people using laptops in coffee shops).
Have you looked into any coworking spaces? They might be able to accommodate you for a few weeks. NYU Poly has incubators on Varick St. in Manhattan, and an office in DUMBO (which I've been working out of for several months). Good luck!
P.S. I know NYU Poly DUMBO has open space, it's in an awesome area, and the management there is friendly.
Second Stop Cafe in Williamsburg. The Ingrid sandwich is good. Everyone there has a laptop and sits and work there for hours. Don't go if you don't like hipsters though. http://www.yelp.no/biz/second-stop-cafe-brooklyn
Just a heads up, most of the Starbucks in Manhattan have removed all their power outlets (last month, or the month before) to prevent people from spending time there working.
I guess having people say "my company started from humble beginning in the local Starbucks" is no longer valuable to them.
I don't blame Starbucks for that at all. I saw far too many people sat there with an empty coffee cup they probably purchased three hours beforehand- they're a coffee shop, not a co-working space.
rubenstein atrium at lincoln center. they're associated with a whichcraft, so you can get food/beer/coffee there if you want, there is wifi, but it's a public space so you don't have to buy stuff if you don't want to.
If your planing on working for a longer stretch (4h) in one location then I recommend the Tea Lounger in park slope. There's a ton of comfy space & lax rules on hanging out a long time.
You can get passes to NYU Bobst library. It is right next to Washington Square Park. Great views, great area, hundreds of iMacs to use if you you want to use more than a laptop.
There's a quaint little gem of a coffee spot in Manhattan (located in Gramercy area) called Irving Place. It's on 71 Irving Place. It's got a great ambience.
(edit): Looks like it's nearly unanimous. Here's a picture for folks who haven't been there: http://nycpano.files.wordpress.com/2011/03/rose-reading-room...