It's only fair to point out the Waxman's former editor's response:
http://www.politico.com/story/2017/10/09/harvey-weinstein-sh...
To summarize: He doesn't remember the conversation in which he allegedly argued that Weinstein wasn't a worthy public topic. And he never met with Weinstein at the Times, as Waxman claims. So it's her word against his. But we can as outsiders consider these assertions:
> Landman also questioned why “if the Times had been intent on protecting Weinstein, wouldn’t it be odd to send a reporter to pursue this story on two continents, at considerable time and expense?’
From the NYT's response (from the current exec editor, who wasn't at the NYT in 2004):
https://www.nytimes.com/2017/10/09/reader-center/dean-baquet...
> I’m sure Ms. Waxman believes she had a story. But if you read her own description, she did not have anything near what was revealed in our story. Mainly, she had an off-the-record account from one woman.
That's not to say that Waxman isn't right on a certain principle: stories don't need to face direct opposition to be "killed". If the NYT had been more open to the idea of Weinstein being a serial abuser, they would have given her more time and resources to pursue evidence that would eventually lead to on-the-record testimony and other hard evidence.
But that's not what you said. You simplified all of the NYT's (and others') inaction to an evil villain picking up a phone and making a threat. What do you mean that the current story came about because "it became absolutely impossible to ignore"? Do you think that it all started with tweetstorms from recent victims? The first story in NYT's investigation involved incidents that were decades old. Meaning that nothing became "impossible to ignore" -- ignoring was the status quo for decades. It's very difficult to square your assertion with the fact that the NYT would've needed to throw considerable money at this investigation to even get it off the grounds.
Sorry to be an apologist for the NYT, but your simplification does a bit of injustice to what the victims faced in the Weinstein scandal, as if they had been complaining on-the-record and openly for decades and they were ignored because of an elite conspiracy. It appears that what they faced was even worse, threats from their own industry and massive personal shame to the point that it was just easier to keep quiet and sign non-disclosure agreements than to speak out about injustice. And Waxman herself would probably agree to this, as she left the NYT to found her own media outlet, which until the NYT's investigation, seems to have completely ignored Weinstein's scandalous history.
In the case of the Indonesia massacre, it's very possible/likely that it was a story that news organizations didn't push hard enough to investigate. That's not at all inconceivable, especially as we see media organizations outright shutting down because of lack of money. But giving your argument the benefit of the doubt, that the media is "consistently doing the government's bidding", then why was it the media that rooted out the Pentagon Papers and the My Lai massacre (the NYT and Sy Hersh specifically for the latter) and published photos that contributed heavily to the public's disillusionment with the war?
But to the greater point: it seems ironic to simplify things into a media conspiracy because of something you read from a Chomsky book, in a thread about an article that hints (based on a recently declassified document) at how perversely/tragically complicated world politics is, even in the face of a massacre. To the smaller issue of media complicity, I'd completely agree that that media organizations have the capacity to act maliciously, or at least be too slow/unprepared to respond to injustice. But that's a result of media organizations -- similar to governments -- being complicated. To reduce the factors of a worldwide tragedy to the consequences of a S.P.E.C.T.R.E. caricature pulling all the strings, ultimately does not help in helping people remember history in order to avoid repeating it.
edit: I gave Waxman more benefit of the doubt before she recently came to the defense of Matt Damon, who was getting criticized as being complicit to the alleged killing of Waxman's story:
https://twitter.com/sharonwaxman/status/917821882556022786
And yet Waxman, an experienced reporter who was writing for her website (i.e. no constraints from ink/paper limits, or overreaching editors), wrote this about Damon:
> The story I reported never ran.
> After intense pressure from Weinstein, which included having Matt Damon and Russell Crowe call me directly to vouch for Lombardo and unknown discussions well above my head at the Times, the story was gutted.
There is no way you intentionally write that about Damon and Crowe, without adding a caveat (e.g. "to vouch for Lambardo as a colleague, though I never asked them about the sexual abuse allegations"), unless you intend to amplify the drama of your own story, i.e. Hollywood's pressure on Waxman. That she only absolves Damon after he gives his side of the story makes me think that she might exaggerate the amount of real evidence she had on Weinstein in 2004 (evidence, again, that she sat on for 12+ years, as someone whose entire livelihood is reporting on Hollywood). But I do agree that the NYT columnist she wrote in response to is "sanctimonious" [0]. Even if that columnist, and his editors, were unaware of Waxman's 2004efforts, they do have current colleagues who cover Hollywood and who most definitely had heard the open secret. I don't agree with you that if the NYT suppressed news about Weinstein out of profit-motive, but I can believe that the NYT could have done more earlier to question someone who happens to be cozy with New York media and media reporters.
[0] https://www.nytimes.com/2017/10/06/business/media/harvey-wei...