I think Nagato/pein>> Naruto at the time of the first fight
Nagato> Naruto at the time of the second fight
and I think Naruto > Nagato currently
K These are my reasons( I know its crazy long)
we all know when Naruto fought six paths of Pein he had a lot of "help" and advantages over pein in intention diffences,most importantly "plot no jutsu" and to top it off "talk no jutsu".
I mean whose to say that EVEN if Naruto does beat all six paths WITHOUT all these advantages (which is highly unlikely in my opinion) that if he touches Nagato Nagato doesn't just absorb some of his bijuu chakra, "un-skinnying" himself so to speak. Then its start all over for Naruto except at "super hard mode".
So I think its pretty obvious that at that point in the story Nagato/pein>>Naruto
now for the 2nd fight with B, Naruto and Itachi vs Nagato, A argument can be made to say that Nagato wasn't truly beaten because he was being controlled, In other words weaker then he would be,
I however see no proof in this and therefore reject it.
It seems that Nagato also effortlessly fought off Naruto and B while Naruto was in KM however this also can't be fully accepted, as their greatest advatage over Nagato (teamwork) was also somewhat of a disadvantage (although how easily Nagato handled them has to take SOME account)
My greatest piece of evidence though for Nagato being better then Naruto at this stage in the story in my opinion is....
when Nagato uses chibaku tensei, Naruto claims that if they(Itachi, B and Naruto) are hit by it they're dead(despite the fact he survived it before

) and I believe if Nagato had fought Naruto 1 on 1 at the time, I believe he would of.
Why else would kishi make it so that all 3 had to fire their best moves (destructive moves of course) at the same time?I know it know its assuming...but use common sense...
I don't believe Naruto had the firepower of a TBB, rasen shuriken and Yasaka Magatama all in one move, at that time.
so if It was a 1vs1 fight Nagato would surly win with just 1 chibaku tensei right?(remember thats him only using chibaku tensei)
and for those that would say that it was EDO Nagato therefor limitless chakra, this is easily brushed off, did he ever really show a multitude or magnitude of techniques that he has never shown before?
all in all I believe Edo or not Nagato "un-skinnied" > Naruto at that point in the story.
Now finally I think Naruto currently in the manga is better then any Nagato "form" we've seen because of his new BM no reason really needed(though in no way shape or form would it be a walk in the park for Naruto).
Although remember we've never seen Nagato TRULY go all out, or Nagato Prime, "mobile" (feat work) with all 6 paths with him and also remember he had mastery of all "mainstream" elemental jutsus
although I still doubt he could beat BM though
