If the NYT had dirt on Republicans, you can bet they have already used it. But your point is probably true just the same. Newspapers have a valuable cash equivalent thing to bribe with: focus and opinion. They don't have to have real dirt to imply and distort. Doubt and suspicion can kill a reputation, especially if it is repeated often enough.
What, if Bush goes after the Times they might give him a bad press?
That shouldn't cut any ice. The MSM could hardly do a bigger smear job on Bush and the Republicans than they are already doing.