As many of the posters have said in one way or another, there are none of what you regard as "active" tribes in Japan. Ainu and other ethnicities that existed in Japan have all assimilated into Japanese culture and lead modern lives.
I've heard a news headline many, many years ago of the death of the last Ainu language speaker. The Ainu language exists only on audio tapes today.
Do you mean 族 (zoku) comes from a term meaning clan or family-group, similar to the Roman gens? I know it currently means "subculture group", like コスプレ族 is something like "Cosplay Club" or "Cosplay Society". What's ながら族 (Nagara-zoku)?
Yes, "zoku" is tribe, clan or race in its original meaning.
Currently, it is very often used from the sociological perspective to describe an emergent or popular type or group of people who share distinctive traits or tastes.
"Kosupure-zoku" is not club or society or any fixed organization but simply the type of people who cosplay.
"Madogiwa-zoku" are people who sit by the window in business offices (i.e., people who have lost the "rat race" for promotion).
"Hills-zoku" are people who live or hang around mostly in Roppongi Hills (i.e., young business entrepreneurs who have become filthy rich in IT, securities, etc.)
"Kauchi-poteto-zoku" simply are couch potatoes.
"Boso-zoku": Mike has already expressed my opinion of them.
"Nagara-zoku" comes from the Japanese "nagara" meaning "while or in the meantime."
Gohan wo tabe
nagara terebi wo miru. (Eat a meal while watching TV.)
This describes a person who does two or more things at the same time. When I was still a student, my friends used to marvel at how I can do my homework while listening to music and laughing at comical antics on TV. Presently, I can only manage listening to the radio or music while working...
The kanji "zoku" is also used in biology to mean "family" and in chemistry for "group (of elements)."
These links are accounts of shows and people doing exactly what you have in mind with the handful of known hunter gatherer tribes left in the world. The closest to Japan most likely meaning a juant through the jungles of Borneo. Ganbattene! 
