There's been quite a bit of shade cast on that article as well. It compares yield growth rates (not absolute yield or cost) across country level data and ignores issues with European production like really high levels of fungicide use. Most people who are in agriculture think that this article was sensationalist crap that exploits several common statistical fallacies.

For more in depth criticism of the NYT article:

http://weedcontrolfreaks.com/2016/10/the-tiresome-discussion...

http://www.npr.org/sections/thesalt/2016/09/01/492091546/how...