saranac brewing company:ithaca beer company:
magic hat brewery:(technically in vermont but i consider them a vassal of new york)
this is one of my favorite beers in fall. it's made with beet juice so it's very sweet and has a funky red color.
wolaver's organic ale:s (also in vermont)
hands down my favorite stout
ommegang brewery:one of the oddest and most complex flavored beers i've tasted. has an average ale taste layered with hints of nuts, flowers, and fruit. very odd but very delicious.
honorable mention:
http://middleagesbrewing.com/i haven't drank any of their beer enough to really rave about it but from what i've had they makes some tasty stuff.