There is some confusion to who to believe the NYT, or elsewhere.
For example check out S.I.'s truth and rumor page:
FanNation | Truth&Rumors | NBA
First article is NBA let ref work under suspicion, while the second is NBA had no knowledge. But they talk about two different things. The NBA was unaware until recently about the FBI's investigation. The NBA was aware that Tim Donaghy was suspicious and hired their own private investigator over a year ago.
All this tells me is that the NBA doesn't even have this excuse anymore: we knew he was suspicious but the FBI didn't have a solid case and asked us not to compromise their investigation.
Edit for clarification: The Denver Post isn't the only place reporting that the NBA new, including other New York papers.