Each character has their own special feats and strengths, so there's no specific order in my Top 5; I don't read much of the Manga either (barring extreme events, such as Sasuke's reappearance). That being said:
- Minato Namikaze:
Truly a genius that appeared once every generation. He didn't possess any special abilities (i.e. Tailed Beast, Cursed Seal, Kekkai Genkai), and yet he was capable of fighting on par with, and eventually overpowering Tobi, who possessed the Nine Tailed Fox at the time. Not only that, but he's the only character I've seen that was capable of sealing a tailed beast near single-handedly (with only Kushina's help) - Even the Akatsuki, who possessed many times more chakra than he did, required 3 whole days to extract/seal a tailed beast. He also possessed quite a strong amount of chakra, seeing as he was able to fight with Tobi & still have enough to teleport and seal the Nine-Tails, though at the cost of his life.
- Itachi Uchiha:
Another genius. Could've been among the most powerful characters, were it not for his fatal illness, inadequate chakra levels, and blindness through his overuse of the Mangekyo Sharingan; and even then, he was still a force to be reckoned with - even Sasuke, at his full power, was incapable of turning the battle in his favor against Itachi, who still managed to one-up Sasuke's ultimate attack, Kirin, with Susano'o, though its use resulted in his death. He's also among the most intelligent characters in the series, among Shikamaru & Shikaku's levels - having forseen that Sasuke would eventually end up taking his eyes and awaken the Eternal Mangekyo Sharingan, he implanted a crow with Shisui's MS in Naruto as a failsafe to prevent Sasuke from destroying the Leaf Village (Although things didn't exactly work out that way). He also has a plan to turn the tables on Kabuto, and while nothing has been revealed about it yet, you'd have to be quite intelligent to figure out how to counter Kabuto at this point.
- Sasuke Uchiha:
Sasuke is among the 'Powerhouses of the Naruto Universe' (i.e. BM Naruto, Killer Bee, A, Itachi, Madara), and with good reason. He was yet another genius of his generation, and has more than lived up to this repuation, seeing as he's recieved praise from various characters (i.e. Orochimaru, Tobi, Itachi) throughout the course of the series and having stood up against quite a few tough characters (i.e. Orochimaru [though weakened], Deidara, Danzo, A, & Killer Bee [At least for a bit]). Being able to create multiple uses from one technique that he was taught is beyond amazing, and his mastery of the Sharingan is not to be overlooked either (seeing as he was capable of making Sai, who supposedly had no emotions, feel fear), though not on Itachi's level (Genjutsu wise, that is). He also possesses an enormous amount of chakra during Part II, having been capable of using all three of his MS techniques simultaneously and consistently, in addition to other chakra-taxing techniques like the Chidori. While we have yet to see his newfound abilities, courtesy of his EMS, it should be expected that Sasuke's newfound power will only add to his already impressive strength.
- Kakashi Hatake:
While many may claim that he's only powerful because of the Sharingan, I disagree; In my opinion, the Sharingan only added to/increased his ability/skills; Kakashi had talent from the start, seeing as he graduated from the academy at the tender age of 5, and became a chunin a year later. Courtesy of his Sharingan, Kakashi is among the few who have mastered more than 2 Elements, as he has access to Lightning, Water, Earth & Fire (Anime-Only) Natures, and has supposedly copied over 1000 techniques. Though through unknown means, he was also capable of Awakening the Mangekyo Sharingan, which deserves credit as well.
- Hashirama Senju:
Little is known about him, other than his famous kekkai genkai, Wood Release & his ability to control the Tailed Beasts; however, seeing as he was able to defeat Madara Uchiha, who had access to both the EMS and the Nine-Tails is an overwhelming feat in and of itself - to this day I have no idea how he could've accomplished this, and I hope Kishimoto will be generous enough to include a flashback of their battle before the series ends.
