Tokyo

I keep putting Tokyo at the top of every list because it has 35 million people in its metropolitan area with an annual GDP of $1.479 trillion.  However, my research into China has convinced me that a tighter definition of "city" should be used when making comparisons.  Suzhou  has its own identity separate from Shanghai.  And I now see Los Angeles as 3 cities:  Los Angeles County, Orange County and Riverside/San Bernadino.  In the US, I use Metropolitan Statistical Area (MSA) as the definition (not CSA), and in Europe the Larger Urban Zone (LUZ).

It's time to apply the same tighter definition to Japan.  Each prefecture making up Tokyo should be treated as its own metro area.  And the other big cities (Osaka, Nagoya) should be treated similarly.

So the list of cities in Japan will be as follows. (This is not a complete list of cities in Japan, just the most important ones).  These are all prefectures, except for Kobe and Sapporo.

1. Tokyo Metropolis (13.0 million, $923 billion)
2. Yokohama/Kawasaki (Kanagawa prefecture), formerly included with Tokyo (9.0 million,  $320 billion)
3. Osaka (Osaka prefecture) (8.9 million, $389 billion) 
4. Nagoya (Aichi prefecture) (7.4 million, $372 billion)
5. Saitama Prefecture, formerly included with Tokyo (7.2 million, $211 billion)
6. Chiba Prefecture, formerly included with Tokyo (6.2 million, $197 billion)
7. Fukuoka Prefecture (5.1 million, $185 billion) 
8. Hiroshima Prefecture (2.9 million, $120 billion)
9. Kyoto Prefecture (2.6 million, $101 billion)
10. Kobe (aka Kobe Metropolitan Employment Area, part of Hyogo prefecture)  (2.3 million, est. $90 billion)
11. Sapporo (Ishikari subprefecture) (2.3 million, est. $90 billion)
12. Sendai (Miyagi prefecture) (2.3 million, $83 billion)

See also Top Japanese Cities by GDP