First, Tokyo Metropolis is not a city. Tokyo Metropolis as equivalent to a prefecture; it was formed by combination of the former Tokyo prefecture and the former Tokyo city. Thus Tokyo Metropolis consist of 23 wards (former Tokyo City) and 26 other cities and towns, villages and islands. So using Tokyo Metropolis is unfair in the city vs city comparison. Only comparing 23 wards of the former Tokyo city may be good, but the GDP figures of 23 wards are unknown.
Second, Nagoya, another major city of Japan, is not on the list. I don't know the exact Nagoya's GDP for 2004, but the GDP of Greater Nagoya was about 400 bilion USD. The population of GN is about 10 milion, and the population of Nagoya city is app. 2.2 milion, app. 1/5 of the entire GN. So if you take 1/5 of GN's GDP, Nagoya City's GDP can be estimated 80 bilion USD, which is larger than Shanghai and Taipei. But in the original post, Nagoya is missing for some unknown reason. If anybody knows the exact numbers for Nagoya, it will be very welcome.