Chocolate factory

Most of the big chocolate houses are in the French speaking part of Switzerland to the west, think Nestle.
There is a chocolate exhibit at the Swiss Transport Museum in Luzern, which I believe would be covered by the Swiss Pass.
http://www.myswitzerland.com/en-us/chocolate-factories/swiss-chocolate-adventure.html

There is also this place in the area.
http://www.myswitzerland.com/en-us/chocolate-factories/chocostud-io-fun-at-aeschbach-chocolatier.html

Have a look at this place Interlaken - it may suit your need:

http://www.schuh-interlaken.ch/en/content/chocolatier

http://www.interlaken.ch/en/the-chocolate-show-interlaken.html

I haven't done the tour, the Lindt-Sprungli factory is near Zurich. My brother enjoyed it very much, and the factory is in a very scenic location on Lake Zurich.