Well lets see.

Rasengan:
Powerful and a deadly move, used by the forth also. We dont really have a good picture of what it can really do since we are talking about naruto using it here.

Chidori:
Looks cool, Seems powerful if it can cut through virtualy everything. But heres a bit of logic.

Chidori(AKA lighting edge) seems like it stabs the person instead if exploding. So it is used for assinations. Seeing how the move hit the water tower: --------| |------> it left a hole. ( Don't know if there was a hole on the other side ) Saying to us that the Chidori goes in like a knife. like a concentrated charka hit.

Rasengan:
The Charka Explodes creating a devistating attack with impact.
-------| | <---This whole side is gone. Seeing how this ability is done, it is greater in combat. But the strain that it gives to the body is very harsh unless mastered.

So in my conclusion it really doesnt matter since both are exceptional skills. there are pro's and con's to both of these Jutsu's