One blemish is not enough to cast away the entire credibility of the source. NYT has published a lot of original reporting that has proven to be true, but of course that doesn't matter on this conversation at all, doesn't it.
It's not just about that, it's more about signal to noise ratio and the impact of their stories. When one deliberately adds a spin to specific categories of news, it's easy to prove them manipulative and thus, not trustworthy. The fact that they currently report correctly on the things outside of their agenda is not that relevant since it's just a matter of time before it becomes their agenda as well. Media should strive for objectivity.