I have seen Confederate flags flown in parts of NJ(more rural southern/central parts) and NY(Mainly upstate and a few isolated examples in Staten Island and Queens from my observation).
This was further confirmed by some friends who attended college and/or go up there every so often for work in upstate NY currently. Incidentally, this is a reason why one doctor friend whose job periodically sends him to the more rural areas of upstate NY counts the days till he can come back to NYC.