What makes you think that? I just skimmed their methodology [1] and didn't see any indication that it's anything other than a list of books that have sold the most (omitting some categories like textbooks).
The interesting thing about the methodology page is that it consistently uses strongly-worded and reassuring terms, but at no point do they mention any numbers or statistics whatsoever. It's made to appear as if they're transparent, but it doesn't actually offer you anything of the sort. Additionally, we can read it and find lines like the following:
>if and when they are included, are at the discretion of The New York Times Best-Seller List Desk editors based on standards for inclusion that encompass proprietary vetting and audit protocols, corroborative reporting
This seems to fit with another quote that a commenter here found for us:
>In 1983 (as part of a legal argument) the Times stated that the list is not mathematically objective but rather editorial content.
On top of this, there's likely to be biases in the information they receive: It's obvious that every large book store in the country (including all digital platforms) doesn't report directly to the NYT, and it would be very unlikely for there to be no bias in which stores decide to work with the NYT or not.
Well, I (am parent^) looked it up. And as a lot of things, that was half right half wrong. Here is a quote from wikipedia
"The list is based on a proprietary method that uses sales figures, other data and internal guidelines that are unpublished—how the Times compiles the list is a trade secret.[3] In 1983 (as part of a legal argument) the Times stated that the list is not mathematically objective but rather editorial content. In 2017, a Times representative said that the goal is that the lists reflect authentic best sellers.[4] The list has been the source of controversy over the years."
[1] https://www.nytimes.com/books/best-sellers/methodology/