It's a hard question. Do we really count Edo Madara as a "ninja", when he's really a medically-enhanced, genetically mutated immortal zombie? He's on a different level from other ninja, because he isn't a normal ninja. The rules don't really apply to him, so it's not really a fair contest.
That said, we haven't seen Edo Madara use certain techniques yet: He hasn't used Amaterasu or Tsukuyomi, he hasn't used most of the Rinnegan techniques yet besides ninjutsu absorbing and summoning that meteor (he hasn't even used shinra tensei yet, which was the one move that Pain spammed the most). He hasn't used any summons except an attempt to summon fox, and Pain also spammed those a lot too. He's basically used Susannoo and wood-release techniques for the most part, with some fire techniques mixed in. This raises the legitimate question about whether Madara is capable of using all these things or if his eyes somehow don't have all the same powers that Pain or Itachi and Sasuke have.
But let's ignore Edo Madara. He's not a real ninja and he could be turned into dust if Kabuto makes a stupid mistake, so let's leave him out of the conversation. Instead, let's stick to real, living ninja that we've seen battle in the "present day" of the manga. Anybody who has been alive during the non-flashback parts of the manga is fair game. This includes Itachi and Nagato, but not Hanzo, Hashirama, Minato, the real Madara, the So6P, etc. This also includes opponents. We're talking about any one "real", "alive" (or, "was alive until recently") ninja versus any other living ninja. We can also talk about people at their prime.
We have a few obvious contenders who seem to come up to the top of most people's lists pretty frequently: Itachi, Nagato, Raikage, Killer B, Naruto, Sasuke, Tobi, Kabuto, Kisami, Kakashi, Might Guy, Tuschikage, Mizukage, Jiraya, Orochimaru, Gaara, Hiruzen and Tsunade. Are any of these people so powerful that they could ALWAYS win?
Orochimaru lost to Sasuke. Sure he was weak, but he did lose.
Itachi lost to Sasuke. Again, the circumstances are a little tricky. Itachi might have thrown the fight and he was definitely sick.
Hiruzen lost to Orochimaru. Did some damage on the way out, but he did lose in the end.
Nagato did lose to Naruto. The majority of the loss was legitimate (Nagato did fight to win until the very end). Considering Nagato was basically immobile and Naruto still apparently had some sagemode/fox chakra left, I think we can assume he would have won.
Itachi seems confident that he can beat Kabuto with Izanami. If that's the case, Izanami seems like it might be a one-time-use trump card. If we're only talking about one battle, MAYBE Izanami means Itachi could always win at least once, but he might go blind immediately after.
Raikage basically lost to Sasuke. He did survive the fight but he did lose an arm and did need to be saved from impaling his stupid butt on an amaterasu spike.
Killer B basically did lose to Kisame. He was saved by Raikage and Kisame switched himself with Zetsu and didn't plan to win. If Kisame wanted to win, I think we all know Killer B would be Killed B by now.
Might Guy beat Kisame, fair and square.
Pain beat Kakashi.
Pain also beat Jiraya.
Gaara lost to Naruto and later lost to Deidara.
Sasuke did basically get beaten by the Kage. He was seconds away from being vaporized by the Tuschikage, and was doing very poorly against the Mizukage. Maybe we don't count this one because it wasn't a one-versus-one battle, but Sasuke was over-confident, he did walk into a stupid situation, and he did almost get himself killed.
The ninja who we haven't seen lose or almost lose a legitimate battle against a living opponent yet are: Naruto, Tsunade, the Tushikage, the Mizukage and Might Guy. If we're talking about a Ninja who could win any battle, this is the short list we have to work with (everybody else has already lost battles, which means they are obviously disqualified). At this point, with the Fox on his team, I think Naruto is the leading contender, but we still don't know what kinds of power Tobi has. Tsunade also does appear to be basically immortal with her regeneration technique activated, so that's something to consider. Neither the Tushikage nor the Mizukage seem like they really are able to win ANY battle, even if they might put up a hell of a fight.
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