If we consider the differences between Kaguya and Momoshiki, I think that we can understand who is stronger.
First, their apparent castes. Kaguya has in all iterations always been depicted as a princess. A princess who became elevated to the station of goddess, put a princess nonetheless. As such, Kaguya would have spent most of her days doing nothing physical, or straining in anyway. She would have no combat training, and truly no need for it, as princesses would be as far away from battle as possible (until castle siege, at which point her life becomes forfeit.) Her rise to power was truly only possible because her species (lets not pretend that Otsutsuki are human) was more advanced than humans (natural, if not able to be accessed byakugan, energy outbursts, knowledge of a tree that would turn one into a god). Eating the chakra fruit turned her into a conduit of at that point unknown energy. She elevated from princess to goddess without having to know how to draw a bow string.
On the other hand, Momoshiki and his partner Kinshiki were depicted as, nobles perhaps, but fighters for sure (their style of dress, training with weapons, etc.) Momoshiki, as a noble male, would have military training and access to more records than a princess. Kinshiki at some point claimed that their powers were ones that they handed down through generations to both preserve it, and also to add it to the next generations base power, strengthening exponentially each hand down. But we are never truly shown them devouring or mentioning having devoured an ACTUAL chakra fruit. He turned Kinshiki into a chakra peach, but this was not something that came from a god tree. This might explain why Kaguya had a rinnesharingan, the peak of that power, while Momoshiki only ever had rinnegan.
In a fight Momoshiki would have the advantage of combat training, tactics, and his rinnegan granted abilities/generational chakra from Kinshiki. Kaguya would have the advantage of being an existence that is solely chakra based. As the mother of chakra, she was able to create a symbiote that acted autonomously but solely for her will, receive and absorb any chakra based attack if given long enough exposure to it (bijuu, amaterasu), with added byakugan and space-time control bonuses. With all this, Kaguya still feared Momoshiki.
The key to this fight was mentioned in the above paragraph. KUROZETSU is the only reason Kaguya would be able to defeat Momoshiki. First, he is an existence that has recorded the entirety of shinobi history. If given enough time to show Kaguya this history (something he planned to do anyway) she would be invincible. She would know of, and therefore be able to replicate any technique. But Momoshiki absorbs techniques? Not if Kaguya used the military knowledge Kurozetsu recorded to instill tactics to her shirozetsu soldiers. They were to be used as fodder regardless, all she would need is one of many shiro zetsu to damage that right hand rinnegan (like Boruto did) and Momoshiki would taken to a different dimension, then be destroyed via the creation of a new dimension (Kaguya's chou gudou dama).
In other words, if Kaguya defeated Naruto and company and had the many years in-between then and when Momoshiki eventually appeared in the canon, she would be more than prepared to defeat Momoshiki. What do you think?
