Had it been someone at WebmasterWorld or some other experienced SEO who questioned the serps, well that I could see.
Could have been that one of our fellow forum posters was doing some backlink research, saw the spammy backlins for JCP, and then dropped a dim to the New York Times. Reporters work on tips from "whistle blowers" all the time.
If you are google, why not just sign up for that link buying service, and then get as many links as possible to a bogus site. Then you could eventually search for links to that bogus site and deduce that all the pages that link to that site are carrying paid links. Then devalue the link juice from those sites.
(I believe the article said that link broker keeps the sites anonymous, so they couldn't just see a list of web publishers and devalue those publishers.)