The two RS Naruto threw were compared to Kurama Mode. Which is the same size as Susano'o. We know how Susano'o compare to a human. Those two RS were huge as **** if you compared to Naruto's body.
Obviously that was Naruto's strongest attack. The 9 Biju RS is limited to amount of chakra the Biju gave Naruto. More than likely Naruto's chakra has to be in sync with the Biju. The fact Naruto only used the biju abilities a few times is proof he doesn't have a lot of their chakra.
The Rasenshuriken Naruto threw allow him to put in as much Chakra and Senjutsu that he can gather.
The only reason the 9 Biju RS did damage to Kaguya is because it reacted to the Tailed Beast within her.