There's quite a bit of Yakuza-related material in older sourcebooks.
- Seattle Sourcebook (FASA 7201) is an SR1 book, and doesn't have much beyond basic description. It's probably not worth tracking down.
- Underworld Sourcebook (FASA 7123) is an SR2 book, but considering that criminal cartels are the core of the book, it's got some good data and could be worth getting your hands on.
- New Seattle (FANPRO 10657) is SR3's equivalent to the Seattle Sourcebook. It's section on the Yakuza is longer, and more up-to-date with the timeline.
- Mob War (FASA 7326) covers the death of a Mafia don, and how the other syndicates (including the Yakuza) react.
As these are primarily source material rather than system material, the edition isn't really relevant. It's all a bit dated, timeline-wise, but is solid from a historical and thematic viewpoint.
- Dark Angel (FASA 7313) features the Yakuza as the primary antagonist.
- Elven Fire (FASA 7310) involves gang warfare, including the Yakuza.
These are both old modules, so the mechanics are useless for SR5. The basic plots could be used, and the characterization and descriptions could be useful.
- Crossroads (FASA 5742) is the only one I recall that specifically involves the Yakuza.
There weren't many written under the FanPro/WizKids label, but I'm reasonably certain none of them involved the Yakuza.
I can't speak to any of the ones written under the Catalyst label; I haven't read them. (I'll try to do some more digging later this evening.)