The only exception is Fukuoka if I recall correctly. Tokyo, Osaka, Kobe, Nagoya, Yokohama, etc. are all on their eastern coast. Is there a historical reason for that?
Actually there's also Kitakyushu, Kumamoto, Niigata, and Sapporo, and you can kind of argue Kobe, Nagoya, Okayama, Osaka, Sakai, and Hiroshima are on the south coast. And Kyoto is of course inland. Saitama too.
The reason why the cities are where they are is geographic: in extremely mountainous Japan, that's where the major plains are. And in this case the Kanto plain cheats by being the largest plain and getting the Tokyo metro area and its 6 cities.