I don't know any particular tour companies but a tour that would take you to Zaanse Schans as well as some of the towns like Volendam, Edam, Marken, would be nice. Touristy, but interesting. And it would be hard work to try and combine those by doing it yourself by buses because the two areas are not very well connected by public transport.
You could also do an organized bike tour out of town with a guide and fellow travelers. Typically these rides take you past cute villages with wooden houses and some farmlands and countryside. Companies are Mike's Bikes, Yellow Bike, MacBike. Reviews for all of them can be found here on Tripadvisor. I'd first check the weather a day in advance though.
Another thing you could do as suggested above is just take a train yourself. For example to open air Zuiderzee Museum in Enkhuizen (1 hour by train) which depicts a small village from the past, fully functioning with craftsmen at work and a classroom where you can take lessons and be scolded by the teacher :-)
The options are numerous. What sort of experience are you looking for?
Edited: 7:11 am, August 24, 2013