As I know that the heroes are always going to be (eventually) victorious, I don't really care how threatening or powerful the villain is in any of the MCU movies. Thus, my main criteria for "best" is simply how much I enjoyed the character on screen.
With that preamble out of the way, my choices are:
Loki (Thor and Avengers) - menacing yet funny and charming
Trevor Slattery (Iron Man 3) - not at all menacing but funny (Ben Kingsley bounding brews while watching football on the telly? Yes, please.)
Grandmaster (Thor: Ragnarok) - Jeff Mother F'ing Goldblum is an international treasure...nuff said.
Justin Hammer (Iron Man 2) - Sam Rockwell...killer dance moves ftw!