In my opinion, Sage Naruto is better. He has high ninjutsu and attack stats. Furthermore, he spawn a clone every time his clones dies, which you c*e it to tank. With his clones up, Naruto ensure a low float which you can combo it off with your team while Jiraya only has a high chance of repulse.
Mystery-wise, Naruto has a lower chakra cost (40) compared to Jiraya (60). It also does lots of damage as well. The only thing is that it does not inflict ignite on the opponent team.
Also, Sage Naruto is easier to pull than Sage Jiraya.