If you know of other documentaries with native Japanese speakers, please post to this thread.
If you are interested in the documentary I watched, Behind the Cove, it is available on Netflix (US) and YouTube ($).
The trailer is viewable on Vimeo: https://vimeo.com/231462289
And there is a short Q&A with the director, Keiko Yagi, on YouTube: https://www.youtube.com/watch?v=7L5GyTu6nrU (there is an English interpreter)