It is difficult to say at this time.
After all, Kisame was making good work of Bee even when using 7 tails worth of chakra even BEFORE merging with Samehada (his sword). And, as the latest chapters have shown, he only "lost" because of Zetsu replacing him with a fake body (which is much, much, MUCH weaker than the original) in order for him to seem dead so he could infiltrate Kumo.
And when you also consider Naruto's moves are pretty much all about chakra AND the fact that Kisame is one of the original hunters of Naruto along with Itachi before (because of his skills, huge chakra, and Samehada), then that also means he has a clear advantage over Naruto or virtually any Jinchuuriki.
naruto and killerbee would win.Naruto would use his sage techniques on Kisame.