They are both natural and correct, as Jonathan says, but there are slight differences:
#1 would be more common to say to a friend, or someone you know. The feeling is that you're surprised about the noise, not who was making it. "It sure was noisy - that was you?"
#2 sounds a bit more like your are surprised WHO was making the noise, more than that it was noisy. "Were YOU the noisy one last night?"
Very subtle difference, but hope that helps!