Starting the question with "who" establishes that you want to know who it is, so if you want to know who is best or the best "Who do you think is the best?" Is the only one that makes sense. You could also say "Tell me who the best is"

Only the first option is correct, the other two are incorrect. You can say, who do you think is the best? Imagine the question is "who is the best"? And "do you think" is inserted because you wanna say, who in your opinion is the best? Who do you find to be the best?

Hey pal. I'm not entirely sure, but I would rather say: Who do you think the best is? The third one, it's kind of weird, thus I just would say: who is the best? Or maybe try a different way to ask that... e.g. In your belief, who is the best? Sth like that. Sorry bro I'm not a native speaker. Have a good day.

Hi there