Because the sound is related to the position in the pedal stroke, I think the BB/Pedals were good first steps... Now that those are out of the way, I would try the other crank, and see whether it fixes things. So, I think you are on the right track.

If it was the frame, I would think that the noise would not be so strongly tied into the position in the pedal stroke, and would possibly make sounds at other times that might stress the joint, such as hard cornering, or other actions that could apply torsional force to the frame.