I think the main question is who had access to this letter?
The actual letter is
here. John Negroponte, Josh Bolton and Steven Hadley were copied on the letter. I doubt anyone in the Bolton or Hadley camps would have leaked the letter. Somebody in the intelligence community with ties to Negroponte's office - possible.
It's also possible that the letter was released as part of a
FOIA request to the Office of the Director of National Intelligence by the New York Times. I'm not sure whether the office would have released the letter, though, and the New York Times makes no mention of making such a request.