There is an interesting bicycle museum in the Netherlands, but it is not located in Amsterdam. It is in Nijmegen, a 1.5 hour train-ride from Amsterdam (plus a 20 minutes' walk to get to the museum).
The museum has an extensive collection of old and special bicycles, including 19th century walking bicycles (pedals were invented later). It shows you about 200 years of bicycling history.
This museum is really outside tourist territory, hence all information in the museum and on the website is in Dutch.