Which source book has the most/best information on the Yakuza in Seattle? The Seattle book, of course has listings of their territorries and the like but I'm looking for something a little more in-depth in their inner workings.

probably the underworld sourcebook for SR2

The Mob War adventure also has some good stuff, but I'd start with the Underworld book first.

Underworld Sourcebook has information aplenty. A little dated, but still good.

Mob War has Seattle-specific stuff, more detailed as to day-to-day Seattle operations but also moderately good.

From memory the Seattle Sourcebook has about a page or so, which is also fairly OK.

The module Dark Angel is really quite good re a run involving Yakuza - one of the few half-decent written adventures (mob war being another).

The Underworld sourcebook is probably the most comprehensive criminal syndicate sourcebook. Other info can be found in any of the various shadows of or target area series of source books. Dark Angel has a bit, the Seattle Source Book(s) do as well. The section on Ryumyo in Dragons of the Sixth World has a little as well.