In fanfiction, it's possible for Naruto to be stronger than Goku. Fanfic writers often tweak the power levels and rules of the characters' universes. For example, if the fanfic writer decides to nerf Goku's Saiyan abilities while enhancing Naruto's Sage Mode and all his ninja skills to an extreme level, Naruto could end up being stronger.
In some fanfics, Naruto can be made stronger than Goku. Fanfic writers have the freedom to manipulate the power levels and abilities of characters. They can give Naruto new and overpowered abilities that surpass Goku's. However, in the original canon of their respective series, Goku has extremely high power levels and abilities that are on a different scale.
One reason could be the variety of his abilities. Naruto has a whole range of jutsu like the Rasengan and Shadow Clone Jutsu. In fanfiction, these could be made extremely powerful. For instance, if his clones could multiply infinitely and each had the power of the original, that would be a huge advantage.
One thing could be unique chakra abilities. If in a fanfic, Naruto discovers a new form of chakra that gives him unlimited power, he could be stronger. For example, a chakra that can nullify all energy - based attacks like Goku's ki blasts.
In a Goku Naruto crossover, both characters have their own strengths. Goku's physical strength and energy attacks are off the charts. His ability to instantly teleport and sense ki gives him an advantage in combat. Naruto, though, has a unique power system. His connection to the Nine - Tails and his ability to use different types of chakra make him a force to be reckoned with. If we consider a battle, Goku's power might seem greater on the surface. But Naruto has the advantage of being able to surprise his opponents with his ninjutsu and clones. Also, Naruto has a strong willpower that has allowed him to overcome many tough situations, which could play a role in a fight against Goku.
Well, in this kind of fanfic, it's not so simple to decide who is stronger. Goku's power levels keep increasing exponentially as he reaches new super saiyan forms. He can destroy planets with his power. Naruto, though, has the ability to harness the power of the nine - tailed fox which is also extremely powerful. Moreover, Naruto has his own unique chakra - based attacks. If they were to fight, Goku might start off with an advantage due to his speed and power. But Naruto is a very quick learner and could adapt during the fight. Also, Naruto has his friends and allies that could potentially tip the balance in his favor in a more complex battle scenario.
In general, it's a bit of a toss-up. The strength of Manga Goku and Anime Goku can vary depending on the specific arcs and battles. Sometimes, it might seem like one is stronger in a particular situation, but that could change in another.