I have always said “Wasn’t it you who _______”; it feels the most natural. However, you use “were” or “are” with “you. Shouldn’t it then be “Weren’t it you”?
We say "Wasn't it you" and not "Weren't it you" because the subject of the sentence is actually it, not you. Think about how you would make the corresponding statement to this question: It was you who _____
It in this case is the actual grammatical subject of the sentence, not "you". It here is an anticipatory "it", which functions as kind of a dummy pronoun. You could also say "You were the one who ____" but "It was you who ____" is a way of emphasizing the fact.