It could be that the times lowered its paywall after Sandy, and only just reinstated it, so people have been able to explore and find more interesting articles than usual.
I've noticed how prevalent the New York Times is on /r/TrueReddit too. I don't think there is a complex answer. The answer to me that is most likely is the simple answer that the New York Times often has quality information and therefore has its articles shared and voted up more.