The answer to this, as with almost everything else in this book, has to do with geography and food production.
According to Diamond, things like germs and technology come to those who get food production earliest. They are able to build large societies and develop technology and political organizations and such. Diamond argues that the Americas were not a great place for food production. There were few domesticable plant species and essentially no large domesticable animals. In addition, the long north-south axis and the many barriers to movement (deserts, mountains, jungles) along that axis made diffusion difficult.
Geography, then, made it difficult for Native Americans to develop food production and it made it difficult for crops and other technologies to diffuse. This meant that American societies had a harder time becoming as developed and advanced as Eurasian societies became.