edit: When it comes to censoring content by political opinion, then I'm more towards the unethical side, but I think it's a step to far to expect any company to allow it's platform to be used to spread attack pieces against itself.
The NYT is a news outlet. They publish what they believe is newsworthy, interpreted with whatever biases they might have. They don't just take random things that other people have published (or want to publish) and publish them.
FB is a social media site. They don't "publish" things; they provide a platform for their users to share things that interest them (and a platform for advertisers, but that's not really relevant here). If a user shares something that praises FB and another user shares something critical of FB (let's assume for the moment that both the praise and criticism are accurate, to preempt the "misinformation" argument), it is absolutely unethical for FB to over-promote the praise and bury the criticism. That's pretty much the textbook definition of unethical.
It's also not done transparently, it would be one thing if FB turned around and outright said "this is inconvenient to our business, so we won't allow you to post it", but in this case they silently downrank the content behind the scenes.
Facebook isn't journalism; it's not comparable. The NYT does publish results of internal investigations into flaws, as do many other businesses, including much of the IT industry (all those open after action reports, for example).
Openness and transparency are necessary antidotes to concentrated power.
Once they are revealed to be acting like a media company, it's a house of cards. Regulation presumably would follow.