Naruto isn't even serious here, he is making small talk with Nagato, and somewhere in his heart he doesn't want to hurt Nagato..
Anyway I would have to make a different thread if I was gonna prove it, so I wont do it here, but the best example is probably the chunin exam where Naruto beats Neji who is labeled as a genius. People just say it was the fox, but that is wrong. Naruto not only out smarted him, he was also able to control the 9 tailed fox chakra during the battle. Even the 3rd hokage was impressed with this, and he was wondering how he learned it, and thought that it was Kakashi. It was in fact Jiraya of course. Even Jiraya was amazed when he trained Naruto and saw how much of the chakra he could bring out (when he summoned giant toad boss first time, and gave him the name BOSS xD ) anyway people keep saying Naruto only relay on the fox chakra, but in most moments of his child hood he was able to control it. Even against sasuke he controlled it when making a tail, and according to the 3rd that should be very difficult.