Ginza has pretty much everything within 500m walking distance. Patek, AP, VC, Lange, JLC, Breguet, Piaget, Cartier, Bulgari, Richard Mille, Roger Dubuis and more for boutiques. Wako carries Grand Seijo and Credor I think. Hour Glass has a ton including Ferrier. Great used stores like Rasin, NJ Time and Cagi Due. There is another one that I can’t remember the name that has a Jean Daniel Roth tourbillon (unless it sold now). Same place has a steel or titanium mock up of the Simplicity case.
Nakano Broadway has a half dozen or more used stores that carry a huge range.
Journe is in Aoyama I think and there is a De Bethune dealer in Shirokanedai.