http://www.businessinsider.com/us-domestic-propaganda-offici...
The closest thing to what you suggest (and it is not that close) is probably Judith Miller's Iraq reporting for the NY Times, but that's mostly down to her incompetence.
I disagree, or maybe Im just poor at searching but terms like "NY Times, government, paying, publish, stories, CIA" I get so much non-relevant search returns its impossible to separate the whet from the chafe. It was also many years ago, so Im sure search bubbles these days will tend to return stories that are newer as a default. The story I am remembering is definitely different from the one you recommended. I wish I could find it, it was a fascinating read at the time.
Not sure it's of major relevance right now, when Trump does stuff that is not the common wisdom of the FP crowd, but normal behaviour should resume sooner or later.
Sort of similar to this as well [2] (very hard to search for 'government pays NY Times, Post WSJ' or 'Pentagon articles in newspaper' etc.... So many results that are not related in whatever search bubble google has me in
[1] http://www.nytimes.com/1977/12/26/archives/worldwide-propaga...
[2] http://www.nytimes.com/2008/04/20/us/20generals.html