Finding a website listing bike parking in Tokyo/Japan turned out not to be as straightforward as I thought (at least, none of my Google queries for the obvious words such as 駐輪場 or 自転車+駐車場 led to anything useful). Local wards (区役所) websites usually have a section for bike parking (bicycle and scooters), but they are not the most user-friendly.
After finally accidentally stumbling on two pretty good sites this morning, I figured I would share my finds with the English-speaking Google world:
Chu-rin.jp has exhaustive listings of bike parking for Tokyo and a few other major cities (Osaka, Kyoto…). Searchable by map or by station.
Cariru-cycle.com (apparently a bike rental website) also has listings of bicycle parking around Tokyo. Not clear if their data is any better/different from chu-rin.jp.
Of course, both of these websites are entirely in Japanese, but not that difficult to navigate even for a beginner.