This is a very frightening statement by the NYT. They are saying that they know more secrets than they wrote about and what they know is even more useful to terrorist (hurtful to the US efforts to stop terrorism on our shores). Does this information consist of agent names, foreign cooperation and methods?
Is this a veiled threat to the Administration to back off any investigation into the leaking of NSA intercepts, "or we will tell all we know and cripple the country's ability to obtain intelligence"?
Whoever disclosed secret information to the NYT should be prosecuted. There is a weak argument that disclosing what was being done is whistle blowing but NOT how we are doing it and by whom.
Remember the J. Edgar Hoover days ?
He had a dossier on everybody.
If the NYT has files on everybody and can selectively leak information to punish or reward, then it becomes a shadow government able to manipulate politicians and bureaucrats at will.