The slide with the explicit formulation was published, written by NSA, that made claims of "not inside companies" much less believable:
"Collection directly from the servers of these U.S. Service Providers: Microsoft, Yahoo, Google, Facebook, Paltalk, AOL, Skype, YouTube, Apple."
This supports the claims of Glenn Greenwald's article and is exactly what companies claimed not existing.
Read the slide: they explicitely name the collecition on the "fat pipes" under other code names. As they have the access to the big pipes, the real time data (c.f. the other slides, earlier) from the inside of companies is certainly unencrypted.