Surprise. Bet you didn't see this one coming, but, yeah, Prendick is the protagonist. Still, sometimes the person telling the story and the protagonist are not the same person (The Great Gatsby and Wuthering Heights are two prime examples).
So how can we tell that Prendick is the protagonist? Because he's the character the reader relates to most. Dr. Moreau's sanity ship has sailed, and we know too little about Montgomery to really connect with him. Prendick's hardships on the island are also relatable to the reader since both know nothing of the island at the novel's outset. This means they get to explore the island and solve mysteries together, like the Hardy Brothers, and run in terror from said mystery like Scooby-Doo and Shaggy. Yep, Prendick and the reader are two of a kind.