If in Minato-ku, I can suggest the "Bike Recycle" sale, held on the second Sunday of each month. Most are your usual Mama charis, but they have a number of road/city bikes for which you must janken. All bikes priced around 9000yen. I managed to get myself a reasonable single-speed to get around town. More info here - be sure to arrive before 10:30 to complete registration.
When I lived in Yokohama I was forced to pay ransom for my son's bike at an impound lot several km away after he had left it illegally parked near a station. I think it was something like 5000 yen. Bikes not bailed out within a month are either scrapped or sold off (some probably to North Korea or such places).