Psst ... Wanna Know A Secret? or ... How's Your Book Selling?
The New York Times receives its info from Nielsen BookScan, which collects book sales data from select bookstores. The NYTdoes not take actual sales into account, only how many books were shipped to those particular stores. (Another secret: top publishers know the bookstores they target and try to make sure a lot of samples go to those stores.)
Keep in mind that the NYT only tracks sales numbers weekly. And, it focuses largely on big name bookstores rather than small indie stores (obviously indies cannot carry every or even a majority of new book titles to determine sales).
This Fast Company article says that it typically takes about 20,000 ordered books during a week's timeframe to have a chance on The New York Times list and the bigger the publisher, the more they'd know about which bookstores to direct samples to:
Amazon uses a different system: it tracks actual sales by the hour.
To find Amazon bestsellers, see the Amazon Sales page on the Author Central feature, which pulls from BookScan:
The NYT numbers are based on anticipated sales for the week, while Amazon's numbers are based on actual sales which are determined by the hour.
Amazon is strictly based on which books have the highest sales:
BookTrackr tracks your book's specific sales: https://www.booktrackr.com
On the BookTrackr FAQ page, note that sales are pulled by looking at places your book is sold. So if publishing on Amazon, it looks at those; if Barnes & Noble, it finds you on NOOK Press and pulls: https://www.booktrakr.com/tour/faqs
Novel Rank also pulls from Amazon: https://www.novelrank.com
Author Imprints also lists a few more sites that allow you to track sales: http://www.authorimprints.com/book-sales-ranking-tracking-tools-authors/
Of the above, BookScan seems to be the most reliable. However, sales fluctuate pretty quickly, which is why it doesn't seem that it, or any other source, can ever be 100 percent accurate.
Barnes & Noble (BAN), Publishers Weekly (PBW), The Boston Globe (BOG), USA Today (USA), The Denver Post (DPO), The Wall Street Journal (WSJ), The Los Angeles Times (LAT), ABA IndieBound (ABA), and WalMart.com (WAL).
Sadly, this article discusses how buying your way to the top is a pretty popular means of getting on the NYT bestsellers list (which also means you need some pretty committed marketing!):
And this article explains it all a little deeper: http://timgrahl.com/the-truth-about-the-new-york-times-and-wall-street-journal-bestseller-lists/
So when is a bestseller really a bestseller? It depends on who you ask.