First of all... Let me set something straight. You're all posting the names of dead people.
People who if were in the top 3 would still be alive.
Hashirama doesn't count, he's dead.
Kakuzu doesn't count, he's dead.
Minato doesn't count, he's dead.
Madara doesn't count, he got beaten into submission by a guy who also died.
My point is... If thy lived up to the hype, they wouldn't be dead. And dnt pull a "Madara got resurrected" fact of the matter, he's still dead and Naruto will make sure he goes back to being dead might I add.
Another thing before I give you my top 3: As shinobi dies, new, stronger shinobi are born. The only shinobi who actually died of old age who was reputable is Madara Uchiha. But again, he's dead.
1. Naruto Uzumaki: Formidable taijutsu, deadly ninjutsu (mastering rasengan earned him this) and he's much sharper than he's ever been.
2. Obito Uchiha: Rinnegan, and Mangekyo combination makes him lethal. Vast knowledge. Monster chakra.
3. Kakashi Hatake: He's practically mastered the Mangekyo and all its attributes, easily on par with Obito now when no one else was.
Notice I didn't include anything about Naruto's bijuu mode and sage mode? That's because he held his own pretty well long before bijuu mode and sage mode. Kakuzu lost to a Naruto who possesed neither of those at the time of his defeat... Someone who ranks in some of your top 3's. So tell me... Naruto being the shinobi he is at this moment in time can kill Kakuzu 17 billion times over with time for some ramen.
Obito is still the beast he was at the time of Itachi's death, when he was untouchable. Master manipulator. Ninjutsu master. Powerhouse. Controlled 6 edo tensei junchuriki at the same time, pushing them to complete tailed beast transformation. Held his own against Naruto, Kakashi, and even the world renowned green beast of Konaha Might Gai. Anyone else would have been dead by the time Madara got there. Controlled the Gedou with complete precision but still fell short against a rasengan.. Placing Naruto above him.
Kakashi has master taijutsu skills, master ninjutsu skills, commendable genjutsu skills. Mastered the lightening afinity, able to use all nature afinities. Owner of one of the only Mangekyo sharingan eyes capable of space time ninjutsu. Master of Kamui, vast chakra reserves, dispite him falling short against Obito. Take note Kakashi isn't an Uchiha, but uses the Sharingan as though it were his birthright. Worthy of the Hokage title as seen when the elders personally asked for him by name.
Disputes?
(but not in 2v1 he lost the fight between the deidara and sasori 
