I've already gone on record saying that I like the idea of a "three-headed GOAT" - and that's pretty much no matter how their final resumes look, unless one is far ahead of the others. But each has their own "flavor of greatness." I also give a nod to Britbox's sentiment.
That said, I have no problem with the idea that Novak's peak form was better than Roger's or Rafa's, except with a couple caveats: One, Rafa on clay is the most fearsome player in tennis history; if we were to split players into their surface components, "Clay Rafa" is the easy call for GOAT. Secondly, Roger at his best was 2004-07...we don't know how that version would have faired against Novak at his best. For instance, imagine 2006 Roger vs. 2015 Novak.
Anyhow, Novak from Paris in 2014 (October) to Roland Garros in 2016 (May) was probably the most indomitable run I've ever seen: 134-9, a 93.7 Win% over a year and a half. Three of his nine losses were to Roger at non-Slams; he also beat Roger six times, with a walkover. Meaning, Roger in good but not his best ever form held his own against Novak at his very best. How would Roger at his very best have faired? We'll never know. But if 2015 Roger didn't embarass himself against Novak at his very best, maybe 2006 Roger would have at least equalled him? I would have favored peak Roger on grass and fast hards against anyone, ever; Novak would have the edge on clay and slow hards.