Bitcoin Forum

Complying (filing for BitLicense)

BitStamp (https://mobile.twitter.com/nejc_kodric/status/630309296245489664)
Coinbase (no recent source, but assuming based on previous comments, e.g. https://blog.coinbase.com/2014/09/10/coinbase-responds-to-new-yorks-recently-proposed/)
Coinsetter (http://www.coinsetter.com/blog/2014/03/11/coinsetter-apply-new-york-state-bitlicense/)
DCG - Bitcoin Investment Trust (https://mobile.twitter.com/DCGco/status/629703816687038465)
MonetaGo (https://mobile.twitter.com/Monetago/status/628612332466405376)

Complying (via trust charter)

Gemini (https://bitcoinmagazine.com/21342/winklevoss-twins-file-trust-application-nydfs-gemini-bitcoin-exchange/)
itBit (https://www.itbit.com/blog/questions-from-the-community-itbits-trust-charter)
Leaving (blocking NY residents)
BitFinex (https://www.bitfinex.com/pages/announcements/?id=51)
Bitcoinpaygate (https://www.reddit.com/r/Bitcoin/comments/3gcedf/bitlicense_the_rundown/ctwu8uk)
Circle? (no recent source, but assuming based on previous comments, e.g. http://www.coindesk.com/circle-bitlicense-block-new-york-customers)
Coinfloor (https://www.reddit.com/r/Bitcoin/comments/3gcedf/bitlicense_the_rundown/ctwwe6s) Blocks all US customers
Kraken (http://blog.kraken.com/post/126244351097/farewell-new-york)
Paxful (http://blog.paxful.com/paxful-cannot-service-new-york-state-residents/)
Poloniex (https://twitter.com/Poloniex/status/627647475638210560)
ShapeShift (http://www.cnbc.com/2015/06/10/company-leaves-new-york-protesting-bitlicense.html)

Zero fucks given (not filing and not blocking):

BitShares exchange?
BTCe?
MPEX (issued its own regulations in response to BitLicense/NSFW)
Any others?

Most of these companies who operate in NY probably didn't had much traction and decided to leave.  They saw that NY isn't worth it and that the process of applying for a bitlicense would been time and money wasting.