Best villain in One Piece? Yeah sure. Best villain in manga? Yeah no.
The best villain in manga is Johan Liebert.
I'll post below info on Johan that I wrote in the past
Johan Liebert is the titular monster of the series. He is the main antagonist of the entire manga.
At first glance, one would describe Johan as a well-mannered, charismatic, and compassionate yet somewhat reserved young man who possesses a plethora of favourable traits and can easily overwhelm individuals with his seemingly flawless nature, as seen with Hans, who describes him as being not of this world. This meticulously crafted facade makes it easy for him to make new allies and manipulate them into doing various deeds for him through the influence of his supposed friendship and good will. With such skill in creating this sense of perfection and pureness, Johan hides his true motives with ease.
Within this contrived exterior, however, Johan callously delivers destruction and suffering to those who happen to fall prey to his schemes. Even before his tenure at Kinderheim 511, Johan still exhibits psychopathic tendencies. For instance, most of his murders, both in childhood and adulthood, have been premeditated and calculated.
Johan often shows a complete disregard for life by pointing to his forehead, inviting Dr. Kenzo Tenma to shoot him.
The product of a clandestine eugenics program founded to create a “übermensch” intended to lead all of humanity, the boy who later came to be known as Johan and his sister were subjected to unspeakable cruelties by their handlers. An uncompromisingly cruel and violent sociopath, Johan’s outward exterior is nonetheless that of a generous and soft-spoken young man with a naturally affable personality. Caught being the split of two dissociative personalities; one sadistic, the other helplessly empathic, Johan’s talent for persuasion is best exemplified in one of his most favorite hobbies: grooming serial killers. Johan possesses an intuitive, almost preternatural ability to identify the latent neurosis of psychopathic personalities, ingratiating himself with them, beguiling them, until finally manipulating them to commit acts of violence on his behalf through a combination of equal parts intimidation and seduction.
Many of Johan's beliefs run consistent with nihilism, as he does not see any meaning to life. He claims, 'Most of this universe is 'death' anyway,' and that to the universe, 'most lives are just specks in a corner of the earth, gone in a flash.'
Johan also has a tendency to make his victims experience the worst possible loss and suffering rather than actually killing them himself; this experience often leads to the victims killing themselves, however. Helmut Wolf is a prime example of this; instead of simply being killed, Wolf is forced to watch as all of his close relatives and acquaintances die, one after another, all so he can feel what Johan felt, solitude.
What is so frightening about Johan is that he possesses this terrifying ability to turn people into monsters using just his words. For instance, he could turn them into serial killers without even lifting a finger. The usage of his manipulative tactics exposes the true nature of humans and using this, he corrupts their souls. In a way, he exposes humanity in its worst image, portraying them as nothing but psychotic killers. Furthermore, these tactics were displayed from an early age, where he was the cause of a tragic massacre at his orphanage, 511 Kinderheim. On that occasion he used stories in order to convince the children that were there with him to murder the staff and then murder each other whilst he was
sitting on his throne and observing all of it. During the massacre in Kinderheim 511 fifty children and instructors were in a chaotic battle, all of them fighting and killing. Whilst all of this is happening, Johan just sits on a throne and watches as the chaos unfolds and the whole orphanage becomes engulfed in flames.
He is a genius-level mastermind with the goal of being the only one standing, although that changes later in the series.
Johan uses his wits to commit his evil with no help from supernatural elements at all. Just with his manipulative tactics, intelligence and the knowledge of how the human mind can be corrupted. Then he executes his plan, creating monsters out of nothing except carefully chosen words. That's what makes him genuinely horrifying. The scary thing about the way this character is portrayed is that a person like this could actually exist in real life, there could be someone out there like Johan in this world. The realism this character expresses throughout the anime really makes you think about the possibility that there could be a person like this out there, which is what makes him that much scarier.
Johan's experiences as a child could make one wonder if Johan is truly THE monster or was he shaped that way by the people around him. In order not to spoil much, I will briefly go through them. Johan was experimented upon and was being raised as the new Hitler by the government. Kinderheim 511, where Johan was sent, was a horrid place where children were treated like criminals and experimented on in an attempt by the government to create perfect soldiers. Johan's mentors had always nurtured Johan's skill for manipulating others with no conscience. However, when confronted, they claimed that Johan was already a "monster" when he first came to the orphanage.
The crucial, defining difference between Johan and others is substance to the claim of his supremacy. Despite all that he was able to accomplish over the course of Naoki Urasawa’s
Monster — manipulating over fifty people to kill one another through suggestion alone, framing the man who saved his life for murder, operating a massive money laundering operation at the heart of Germany, and coordinating a shadow network of killers to do his bidding— Johan has no special abilities to speak of, save for intelligence. No magical notebook capable of killing anyone whose name is written in its pages, no unholy totem gifting him with the blessing of divine fate, no special devil fruits that bestow magical powers, nothing. He is a human being, no more and no less, and that is precisely what makes him so terrifying. Furthermore, he exemplifies best the key idea that evil, far from being a vast and inhuman concept, is actually intimate. He is as a spider, weaving a web of criminality and chaos wherever he goes. Finally, he is, without question, a monster.