First off NMAI has an awesome online course on American Indian languages and how they played a role in US history. They even include a section on Code Talkers, go there now and check it out!!
I tried to find a good map that shows all the NA languages on the North American continent and my google-fu failed me. So the maps here are meant to give you a general idea of what languages were spoken before contact and that may remain now. Many tribes are now engaged in a desperate race to save their languages. Some only have a handful of speakers left. Many tribes are using immersion to teach their languages to the next generation. Here's a link to an interesting article on NA sign languages.
Now on to the maps!