I think it was Peter. The thing is that that exact event (him activating the machine) was what changed the timeline. But that doesn't change who did activate it.
The main issue regarding this matter, is the fact that we are stuck in a paradox. Much like the creation of the machine itself: it is not certain who created it, but it was sent to the past by Walter, through the wormhole in Central Park Over There (in this transcript of the last episode of season 3, look for "Peter's Residence - Time Paradox"). This means that this loop would repeat itself, thus, the machine would not actually have been created. It was just there. At least I think this makes sense... but do correct me if I'm wrong!