One can easily imagine reading an article like this published on a Russian site, with 'Kaspersky' replaced with 'Symantec' and 'FSB' with 'NSA'.
TBH, regardless of the NYT and their recent "red-scare", I'd be concerned with using them on sensitive systems -because either knowingly or unwittingly they could have FSB moles working for them.
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.