Actually Indra's Arrow is Sasuke's strongest attack. It was fueled by the bijuu chakra sure much like Naruto's twin Rasengan were fueled by NE from the entire planet.
Indra's Arrow's power w/o the Bijuu's chakra hasn't been seen, so it's an unknown variable not worth mentioning. Nor does anyone even know with 100% certainty if he can use it without said power.
In a clash against chidori Naruto's Rasengan Shuriken holds the elemental advantage over chidori. Let's not forget that Uchiha chakra is more potent. It becomes a matter of Quality over Quantity.
When Sasuke added his Enton to his chidori in their VOTE 2 clash they equaled out as Sasuke them had the element advantage over wind.
Both have Jutsu that are more powerful than the others depending on what they mix into it at the time.
So? That isn't Bijuu Dama. And no, Sasuke's Enton Rasengan was equaled by Naruto's Kyuubi Rasengan because they are simply that powerful. Rasengan obviously isn't wind so I don't know where you are getting the element advantage stuff from.
Sasuke's Chidori can not increase in power more than Naruto's Bijuu Dama can thus Naruto is stronger than Sasuke. The only unknown variable is Indra's Arrow.
Though I will say that if he can use it on his own, but on a smaller scale, it'd be equal or stronger than Naruto's Twin RS w/o the world's Nature Energy.