The most important geographical advantage that the people of Western Europe had came from the fact that Western Europe was connected to a huge landmass with a large population. This was the main geographical factor that gave them an advantage over the natives of the Americas.
The fact that the Western Europeans were connected to a huge and populated landmass gave them two major advantages. First, it gave them many more sources of technological and other innovations than the Native Americans had. The Western Europeans could borrow from many sources (for example, by getting the idea of gunpowder from China). Second, it brought them into contact with more epidemic diseases. By the time they made contact with the people of the Americas, the Europeans carried many diseases, like measles and smallpox, that could devastate populations that had no immunity. The Americans had essentially no similar diseases that could harm the Europeans.
Thus, the geographical advantages the Western Europeans had were ones that made them more dangerous to the people they encountered in the Americas and elsewhere.