In terms of just skill and not kekkei genkai or jinchuuriki it would be:
1. orochimaru- studied everything there is to know about jutsu; medical ninjutsu, forbidden jutsu, sage techniques, etc.
2. minato- mastered FTG, created rasengan, and learned sealing techniques of the Uzumaki clan
3. ohnoki- uses very powerful dust style, faced Madara before, recognized the errors of his past, strong enough to stay alive after many many years.
4. tobirama- created edo tensei and FTG but wasn't strong enough to stay alive
5. kakashi- skilled use of the sharingan even though it isn't his, created chidori, very smart ninja and adaptable.
In terms of ninja with kekkei genkai it would have to be Madara hands down as number One: He pretty much knows almost every jutsu, he was skilled enough to plan a way for him to be resurrected after he died through Zetsu, his rinnegan, and obito. Next would be Itachi for just about every reason too. I won't go further.