It's all about focusing on the priorities. The administration has their hands full with the WOT and it's multiple fronts.
An investigation of the NYT would be a further distraction and the NYT's constant ankle biting is starting to backfire on them.
What we are seeing here is the NYt's increasingly desperate attempts to be relevant.
If their hands are too full to prosecute illegal dissemination of classified data, they need to set some things down. Somebody in the administration needs to lose their clearance & go to jail. I'm not sure how the prosecution of a corporate entity (the NYT) would work.