I'm glad that you're out of your hiatus, but Kisame was talking about Jiraya and not Naruto/Kurama I'll explain why.
Let's get the context right by inserting the right names in the conversation.
"Even if you might be able to take Jiraya on, I'm not so sure about me. Jiraya's in a different league."
"It was great finally finding Jinchuriki at the ramen shop, but.. Jinchuriki's babysitter was one of the three great shinobi of konoha legend"
Now, those two(Kisame and Itachi) were observing Jiraya and Naruto from that cliff and going back and forth by looking (say pointing) at them and talking. So the first sentence HIM and HE'S is when Kisame is looking (consider pointing) at Jiraya and then in the next time he's speaking about Naruto after looking at him (consider pointing at). And the conversation makes complete sense without any speck of doubt.
One more important thing that we should not forget is that the Tailed Beasts were always referred as
'IT' and never
'HIM' or
'HER'. It was only post the War Arc Naruto started to refer them as HIM/HER. So if Kisame was really talking about Naruto's Kyuubi then he'd said;
"Even if you might be able to take IT on, I'm not so sure about me. IT's in a different league."
but that's not what happened because he was talking about Jiraya. The Anime made it very clear that it was about Jiraya as well.
One more thing let's not shit on Jiraya by saying Kisame takes him High diff etc, because Kisame never could hope to defeat 7th Gate Gai who was on par with Kamui Kakashi as witnessed in war arc. And Kakashi openly admitted being lesser than Jiraya before war arc.
And finally, words of wisdom by none other than Akatsuki Leader:
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