Wait. If i remember right when sasuke and Naruto fought on top of the building and they both penetrated the water container Rasengan did the most damage than Chidori. But again I think they have there places where they excel at.
Rotation is tricky though. Nothing to my knowledge has ever stop rotation the only thing that depends on rotation is the users chakra or stamina. So I don't think chidori can pierce it. Rasengan can maybe push it back.
Remeber Rasengan rotates so maybe it will force it the other way and stop it.
Think of a ball spinning around very fast then think about a pin trying to bust it. Odds are the pin will keep slipping. Now same situation think of another ball (rasengan) rotating the different way trying to stop it. Push back or it stops it.
Most logical answer I can think of using science...
p.s If going by manga Rasengan>Chidori, If going by the knowledge of kaiton. It might the the best defense against anything but it has a duration and depends on the user.