In A Separate Peace, Gene functions as the narrator and the protagonist while Finny is an important character (but not the protagonist).
Gene reflects on his feelings and his thoughts throughout the novel and, importantly, offers the context of the story in the first chapter: The story to be told in the novel is his story.
A Separate Peace is structured in a way that puts Gene in the middle between Finny and Brinker, the two characters who can be said to represent childhood and adulthood.
Finny is characterized by play, imagination and innocence while Brinker is characterized by seriousness, organization and drive. Brinker wants to enlist early and Finny wants to pretend there is no war on.
Gene believes that he must choose between these two paths and this choice is one of the underlying conflicts of the novel. All the other conflicts and episodes of the novel also concern Gene, while not all of them concern Finny.
Gene visits Leper and Finny does not. Gene meets Brinker's father while Finny does not. Gene is always present in the story and Finny is not.
All these facts definitely show that Gene is the sole protagonist in the novel and Finny is an important and symbolic character in the text.