Speaking for myself, and only for myself, no I think the NYT is not fair and balanced to Clinton. I don’t know where your they have “vendetta because she won’t talk to them and treats them like she thinks they are stupid” comes from though other than your own fevered mind.
The NYT is not all of mainstream media of course: large portions of the mainstream media are no more biased against Clinton than they are any other frontrunner. Not counting the Fox ilk of course.
I also believe that mainstream media in general will be biased to stories that potentially bring down a clear frontrunner.