I would guess that it is a combination of "nerd" - a person who is smart in school, but socially awkward and "amigo" - Spanish for "friend". It would mean two or more friends who hang out together and are nerds (or nerdy).

It's a combination of "Nerds" and "Friends" in Spanish. It's also the name of my webcomic :) http://nerdmigos.blogspot.com