Are you sure it is bias or justified criticism? From my POV, the "bias" always seems to me to be justifiable criticism of Trump. I mean, the man lies so frequently it's almost impossible to present "his side".
I worry when I see these comments. They seem to make the same mistake that the BBC did when they presented equal time to climate change deniers as they did to climate change scientists.
I think your latter point is one of the defining sociocultural challenges of our time. We have stressed openness and fairness in public discourse to the point of enabling actors who 1) seek to undermine that public discourse 2) hold positions that are really spurious in relation to the discussions we need to be having. E.g., the public should be arguing over how to respond to climate change ---especially the social and economic trade-offs that might be necessary--- rather than about its existence.
NYT went berserk after the 2016 elections if you ask me. Now every article feels like an opinion piece.