Depends whether we are talking best actor's portrayal of a villain, or just best villain fullstop.
Actor: Anthony Hopkins in SOTL, although some might argue he is an antihero rather than a villain
Villain: Darth Vader is pretty hard to beat; I think the fact that he is masked just adds to it, placing more emphasis on what he says and how he says it. He is also multi-faceted.... he is good in combat, can use force powers, has a large navy at his disposal, yet can also try to use powers of persuasion.