In what way is NYT not an independent news source? It's not owned by some giant media conglomerate, it's family owned. And last I checked it was one of few media companies reporting good financial results, not cutting costs.
So arguments like this article, even cloaked under “opinion” don’t carry weight because it’s just propaganda to sell more papers.
There's nothing about those things that is mutually exclusive. If your entire business depends upon you being a truth teller it is in the interests of both the company and your shareholders for you to tell the truth. Manufacturing a story could be devastating for NYT's reputation, and consequently for their shareholders.