At what point does Naruto surpass Kakashi? When I see lists where they rank most powerful shinobi in Naruto, they generally rank Naruto near the top (usually 1 or 2). These lists generally don't even have Kakashi in the top 25, yet Kakashi is a Jounin, whereas Naruto has NEVER even been able to become a Chunin!

So at what point in the show is it that Naruto surpasses Kakashi?
This is highly opinion based question. The lists you might be referring to are mostly personal rankings by individuals who are using bias/potential to rank individual Ninjas. For Example, Ina-Shika-Cho may be great in a team, but lose out individually. However, I'll try to answer the question based on canon information only.

Naruto surpassed Kakashi in terms of Raw Strength and power as a Ninja, when he mastered the Wind Style: Rasenshuriken. This is proven by the fact that he defeats a Ninja Kakashi had trouble with in his 2nd attack and pretty much one shots him.

This was an achievement that showcases Naruto's persistence and talent as a Ninja, creating a move that both his Father and Sensei (Kakashi, Jiraiya) couldn't do. 
He had been moving up the chain for several instances (like defeating Itachi duplicate), but this is the most clear demarkation of his prowess is beating Kakazu 1v1 with his Rasenshuriken. This is further proven by the fact that Kakashi himself said it wondering if Naruto had surpassed him. .

Later also Kakashi admits to Naruto, that he might be even stronger than him now. 

Finally, The moment where everyone acknowledges Naruto's strength and talent is clearly beating Pain. Jiraiya and Kakashi died fighting Pain, while Naruto was able to beat him soundly. This moment, leaves no premise for confusion. So somewhere between Kakuzu and Pain Naruto had surpassed Kakashi!