It is, in fact, a cluster of municipalities. Tokyo isn't considered a city anymore but a megalopolis.

Per Wikipedia:

  Since 2001, Tokyo consists of 62 municipalities: 23 special wards, 26 cities, 5 towns and 8 villages. Any municipality of Japan has a directly elected mayor and a directly elected assembly, each elected on independent four-year cycles. 

It's interesting to see when you cross from "neighborhood" to "neighborhood", how things change as if you were in the outskirts of a city and then back to a busy center again.