Well Jared Diamond is referring to individual intelligence, not the wisdom of their cultural practices.

More specifically, he states: "My perspective on this controversy comes from 33 years of working with New Guineans in their own intact societies. From the very beginning of my work with New Guineans, they impressed me as being on the average more intelligent, more alert, more expressive, and more interested in things and people around them than the average European or American is. At some tasks that one might reasonably suppose to reflect aspects of brain function, such as the ability to form a mental map of unfamiliar surroundings, they appear considerably more adept than Westerners. Of course, New Guineans tend to perform poorly at tasks that Westerners have been trained to perform since childhood and that New Guineans have not. Hence when unschooled New Guineans from remote villages visit towns, they look stupid to Westerners. Conversely, I am constantly aware of how stupid I look to New Guineans when I’m with them in the jungle, displaying my incompetence at simple tasks (such as following a jungle trail or erecting a shelter) at which New Guineans have been trained since childhood and I have not."

Jared Diamond's whole thesis in Gun, Germs etc is post hoc ergo propter hoc.