I have no idea one way or the other (regarding either the NYT or Kaspersky). But it does strike me that your theory is credible.
However it also seems credible that Microsoft, Intel and other critical hardware and software vendors based in the US may have moles and/or agreements in place with CIA/NSA.
That's possible as well but if you are US based at least the damage is contained --the NSA isn't going to give your data to a foreign competitor (or local for you have recourse in the legal system), whereas I'm not so sure the FSB would not "share" information with their preferred firms and if you become aware of it, you would have very little recourse.
Unless you aren't in the US or Russia, then you have Russia potentially spying for Russian companies/government, and the US/NSA potentially spying for US companies/government. The NSA has been caught with their hand in the cookie jar when it comes to corporate espionage[0][1].
I think it's common knowledge industrial espionage is practiced from time to time by all major powers. The question is a calculus. Who'd put you in a smaller/bigger ditch, relatively speaking.
