Nagato is more powerful than the Pains, however since he's immobile he's still vulnerable to strategies like Jiraiya's one to take away the pains vision, Naruto's ones of distraction or Itachi's. strength is the not the same as power, the six paths of pain are still more powerful than any other shinobi outside bm naruto, madara, hashirama and juubito. and their linked vision and superior numbers give him an almost unassailable advtange.
also, that naruto defeated pain means little. a. he had a lot of accumulated knowledge which counts a lot in pain's case where his mystery is one of his strongest assets. b. the deva path wasnt functioning for most of the fight (imagine say itachi w/o susanoo in the sasuke fight, he'd be a little pile of ash right now) and c. naruto survived mostly because he went full kyuubi.
the only persons Pain would definitely not beat are current Naruto, Hashirama, Juubito (or any version of Obito really) and Madara. DSM Kabuto, EMS Sasuke, prime Hanzou and Minato are doubtful, maybe Hiruzen once Kishi decides how powerful he really is. so he's still top ten easily.