It commits the post hoc ergo propter hoc fallacy. It's also teleological. What Diamond is saying is that because the West ended up on top, the West
ended up on top, and this type of path dependency simply doesn't stand up to historical or theoretical scrutiny. Diamond might be correct that the West had certain conditions and the rest of the world had other conditions, but he can't prove those conditions were specifically responsible for the West's development and other places' lack of development. And as I recall, several ancient history specialists also don't think very highly of the accuracy of the material in his book.
For some examples, if the West was destined to success, why was China the most powerful country (loosely defined) in the world for the first 3 millennia of Western civilization? Can we really attribute the West's rise and China's decline to geography or agriculture? Why did Iberia go from the poor brother of other Western countries from the inception of Western civilization until 15th century or so, then dominate most of the world several centuries, go back to being dirt poor (by Western standards) for centuries after that, and finally almost catch up to the other Western countries in recent years? What about Japan, which has always lacked resources and probably has the worst geographical position from any major country in the world? Did this cause it to be poor until the 19th century, become fairly well off in the early 20th century, become poor again until the 1970s, become wealthy in the early 1990s, and slide back to mediocrity today?
Ultimately, foreign policy is determined (in the long term anyway) by its power relationship to other countries, which is in turn determined by its economic growth. To the extent that geography can influence long-term economic growth, it does have an influence on foreign policy. But it's one domestic factor out of many, including things like domestic stability, culture, etc. And even then, those factors must be compared to those of its neighbors. By the way, Diamond's theory isn't quite as bad as those of the geography school (to which the Nazis subscribed by the way, which is not to say it's some evil theory but it's interesting nevertheless), since it looks not only on countries' geography, but also things like agriculture and population density.
I'd recommend everyone to read Gilpin's War and Change in World Politics.
Most IR people have some disagreements with parts of the books, but there's widespread agreement its main idea.