Itachi/Kisame
It would seem that Itachi would be able to locate Nagato by seeing where the chakra signals are eminating from. So that's the easy part. The hard part is taking out the six paths that would be standing in their way.
Itachi has already shown to be able to outmanuver the rinnegan, so we know he can at least land a hit or two. And in theory, Samehada could be used to break the chakra connection between Nagato and his paths by absorbing the chakra being sent to the paths - that is, if he lands a hit on one of the paths, Samehada would suck Nagato's chakra through the rods (and yes, I know it's not exactly the same as using puppets).
That being said it would definitely be a close fight - but I see the Itachi/Kisame team winning since Itachi would be able to gather intel quickly.