The yakuza are more active in southern Japan, particularly Kobe and Kyushu, than in Tokyo, although they can certainly still be found in the nightlife districts.
In general, they're also far less powerful than breathless Western reporting (including Gibson's portrayal) tends to make them out to be, in part thanks to a persistent multi-decade police crackdown.
They mostly run construction companies now, an industry where there's been a wild amount of corruption for a long time- in part why most rivers have completely unnecessary concrete banks, ostensibly for "flood control". See "Dogs and Demons" by Alex Kerr (http://alex-kerr.com/html/dogs___demons__english_.html).
Anecdotally, I know someone who owned a house in Okazaki (a city outside of Nagoya). Someone decided they wanted the land for a construction project, so they resorted to threats to get him to move- such as smashing his car windows. No way that was a random punk smashing windows- when I lived in Okazaki, a defaced public bathroom would make the local news. Classic Yakuza tactic, and unfortunately he ended up moving because of it.
That's fascinating, there was certainly no shortage of concrete in the places I visited in Japan. I got to wondering just how much concrete dust must be in the river sediment.
if it is anything to go by (probably not), most Yakuza stories in mangas are about collapsed clans surviving or waning organizations trying to rebuild a mafia rule
In general, they're also far less powerful than breathless Western reporting (including Gibson's portrayal) tends to make them out to be, in part thanks to a persistent multi-decade police crackdown.