Naruto is controlling it inside his body , Sasuke controls it outside his body ( in the atmosphere )
Senjutsu cannot be used outside of the body unless the user is in Sage Mode and first draws in the natural energy. Here is a little info about it from the wiki:
"Senjutsu practitioners
learn to draw the energy of nature inside of them, blending it with their own chakra (created from spiritual and physical energy within the shinobi). This adds a new dimension of power to the sage's chakra, resulting in the creation of "senjutsu chakra." This new chakra enables the user to enter an empowered state called Sage Mode, which can then drastically increase the strength of all ninjutsu, genjutsu, and taijutsu."
Kirin = Natural energy + Chidori ( a Normal Chakra base ninjutsu ) to controls it and shaping it into a Dragon.
And Normal Chakra = Spiritual energy + Physical energy.
Kishimoto > you.
Sasuke only uses shape manipulation to mold Kirin after the formation of the storm clouds. He does not necessarily use Chidori to do so. Not to mention that Kirin must first have the storm conditions available, whether already existent or created by Sasuke.