This is honestly a very hard choice.
Yeah, you could argue that Itachi beat Nagato after he was revived by the Edo Tensai, but that was because his body was frail and slow.
During their prime, this is a very hard choice to make. I don't think Izanami would affect Nagato. Izanagi (if Itachi can even use it) can only be used twice before he's blind. (Once if he wants to keep his vision). Genjutsu COULD work if Pain doesn't see it coming, but I'm pretty sure he would from a Sharingan user. Amaterasu and Susano'o are the only real trouble he's going to have to deal with. BUT, he can outrun the sword of Totsuka, probably absorb Amaterasu, and counter in many ways.
It would probably be a close fight, but I would have to go with Pain.