Eric Lichtblau, who covers the Justice Department for the Times, has an article up on Slate's front [1]page [1], adapted from his upcoming book "Bush's Law: The Remaking of American Justice," accusing the Bush administration of lying to him about its anti-terrorist surveillance programs. 
You may remember that Lichtblau and Times colleague James Risen broke the news [2] about theclassified National Security Agency's wiretapping program in December 2005, with a scoop to be included in an upcoming book by Risen (a detail the Times left out of its initial article). Six months later those same two reporters made an even more egregious revelation of classified information,revealing classified details about SWIFT, a U.S.-instigated international bank surveillance program.
Describing a tense pre-publication meeting in the White House, Lichtblau basically admitted the paper's bias against Vice President Dick Cheney:
For 13 long months, we'd held off on publicizing one of the Bush administration's biggest secrets. Finally, one afternoon in December 2005, as my editors and I waited anxiously in an elegantly appointed sitting room at the White House, we were again about to let President Bush's top aides plead their case: why our newspaper shouldn't let the public know that the president had authorized the National Security Agency, in apparent contravention of federal wiretapping law, to eavesdrop on Americans without court warrants. As New York Times Editor Bill Keller, Washington Bureau Chief Phil Taubman, and I awaited our meeting, we still weren't sure who would make the pitch for the president. Dick Cheney had thought about coming to the meeting but figured his own tense relations with the newspaper might actually hinder the White House's efforts to stop publication. (He was probably right.) As the door to the conference room opened, however, a slew of other White House VIPs strolled out to greet us, with Secretary of State Condoleezza Rice near the head of the receiving line and White House Counsel Harriet Miers at the back.
....
By 2004, I had gained a reputation, deservedly or not, as one of the administration's toughest critics in the Justice Department press corps; the department even confiscated my press pass briefly after I wrote an unpopular story about the FBI's interest in collecting intelligence on anti-Iraq war demonstrations in the United States. To John Ashcroft and his aides, my coverage reflected a bias. To me, it reflected a healthy, essential skepticism - the kind that was missing from much of the media's early reporting after 9/11, both at home in the administration's war on terror and abroad in the run-up to the war in Iraq.
That shared skepticism would prove essential in the Times ' decision to run the story about Bush's NSA wiretapping program. On that December afternoon in the White House, the gathered officials attacked on several fronts. There was never any serious legal debate within the administration about the legality of the program, Bush's advisers insisted. The Justice Department had always signed off on its legality, as required by the president. The few lawmakers who were briefed on the program never voiced any concerns. From the beginning, there were tight controls in place to guard against abuse. The program would be rendered so ineffective if disclosed that it would have to be shut down immediately.
All these assertions, as my partner Jim Risen and I would learn in our reporting, turned out to be largely untrue. ....
We went back to old sources and tried new ones. Our reporting brought into sharper focus what had already started to become clear a year earlier: The concerns about the program - in both its legal underpinnings and its operations - reached the highest levels of the Bush administration. There were deep concerns within the administration that the president had authorized what amounted to an illegal usurpation of power. The image of a united front we'd been presented a year earlier in meetings with the administration - with unflinching support for the program and its legality - was largely a façade. The administration, it seemed clear to me, had lied to us. And we were coming closer to understanding the cracks. By the time we met with White House officials in December 2005, Keller had all but made up his mind: The legal concerns about the program were too great to justify keeping it out of public view. The only real question now was not whether the story would run, but when.