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WARNING: This is all second hand information I gathered when researching gyms for my brother very recently. Please take everything with a grain of salt as I've never attended any of these gyms, and if anyone has any corrections or additions, go right ahead.
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Coban's place is relatively new and certainly worth checking out. Everything I'm reading about it is positive, with not one negative experience. Whenever you have someone like Coban teaching classes, it's at least worth a peak.
The three established powerhouses in NYC, of course, are The Wat, Five Points Academy and Evolution Muay Thai. The Wat is (*generally*) considered the best of the three, Five Points Academy has the best facilities and a massive open gym, and Evolution Muay Thai is a good combo of both, more welcoming to the inexperienced. There's also Chok Sabai that I've heard good things about, and it attracts a sizable amount of good looking women.
If you can make the trip, Sitan's in Astoria Queens is widely considered the best Muay Thai in New York (even though it has more of a dutch flavor to it), but if you're coming from Manhattan, you may be spending more time on the subway than actually training, and Sitan's schedule isn't as flexible as the NYC gyms.
Borodins in Brooklyn is supposedly very good as well, but the Manhattan gyms are on par, and the trip can once again be kinda painful depending on where you are.
For the MMA swing of things, Renzo Gracie Academy, and Camp Undefeated both have great Muay Thai coaches (I believe Renzo's instructor came from The Wat). So if you want to throw in some BJJ/Wrestling/MMA in there, these may be your best bets. Actually, New York Jiu Jitsu may have some great Muay Thai coaching but they seem to drive away their MT trainers every year.
There's supposedly very kickboxing oriented Kyokushin dojos in NYC too, but Kyokushin isn't very beginner friendly.
Also, from what I gather, stay away from NYSanda unless you wanna just take the one free class deal.
Hope that helps.