The major methodology that Diamond employs in this book is taking anecdotes and trying to make broader theories from those anecdotes. This is a way of thinking known as "inductive reasoning."
Diamond takes a number of anecdotes about history and studies them. By "anecdotes," I mean events that happened in history, such as the defeat of the Moriori by the Maori. He then tries to construct a broad theory that accounts for all of these anecdotal events.
Historians have to use anecdotal evidence. They cannot look at everything that ever happened, so they have to pick specific events just as Diamond does. What makes Diamond's methodology different from what many others have tried to do is that he then uses inductive reasoning to try to arrive at overarching laws of history that have determined the course of human history.
Diamond's major methodology, then, is inductive reasoning. He takes specific historical events and tries to construct laws that would account for those events.