1. SO6P, he created ninjutsu and was the ten tailed jinchuriki.
2. Nagato, with the six paths of pain I don't think anyone one man could have gone into battle with all 6 at once and been victorious (unless they knew the secret to his technique), because where one path has a weakness it is nullified by one of the others strengths(eg animal path weak against close quarters combat, the almighty push doesn't allow anyone to get close)the six paths went into the leaf and took everyone on and a one of the paths destroyed the leaf with a single jutsu, then had enough strength to battle the nine tails alone, then revive everyone he'd killed. Madara did manipulate him yes, but Pain was the Akatsuki leader and Zetsu was shocked he could be defeated by anyone even in a weakened state.
3. Minato, no flaws to any of his techniques have been seen by us yet, and seemed to take on Madara + the nine-tails at the same time without really being pushed to his limit
4. Madara Uchiha, very smart, very advanced space-time ninjutsu, posseses eternal mangeko sharingan and rinnegan. But I can't help thinking that there's something we don't know about him, a weakness maybe he's always so reluctant to fight, Pain went into the leaf and crushed it alone, what's stopping Madara from doing the same?
5. Hiruzen Sarutobi, I hear everyone saying Senju Harashima, did they forget the an old weak Hiruzen Sarutobi taking on the first and second hokages and Orochimaru all at once. He even manages to seal the two kages before robbing Orochimaru of his ninjutsu.
Honourable mentions include:
Raikage - Fastest shinobi alive, lightning armour + body flicker technique
Killer Bee - Tailed beast bomb, friends with his tailed beast, and not as stupid as everyone makes out
Kabuto/Orochimaru - IWR very powerful (I doubt we've heard the last from Orochimaru)
Itachi- Very smart, great genjutsu but , nobody remembers his low stamina.
Deidara - Very underrated, was only 19 and was very powerful and a great tactician, trained one of his eyes so it was invulnerable to the sharingan, and nobody would be able to escape or survive his final explosion unless they possesed a spacetime jutsu or izanagi.
Hanzou- Not much seen, but beat down the three legendary sannin at once.
Ginkaku + Kinkaku (Just complete legends)
Naruto - Kyuubi, Sage mode, advanced rasengan techniques, tailed beast bomb
Sasuke - Eternal Mangeko Sharingan, second person to awaken it, Susano'o, Amaterasu etc
Konan - Greatly wounded the infamous Madara Uchiha and gave us info about the limits of his powers
Jiriaya - Loved his 'research' LOL, one of the legendary sannin, vast array of jutsu, managed to capture one of the Pains, and his apprentices speak for themselves; Minato, Nagato, Konan, Yahiko and Naruto
