In any COOP supermarket you will Lindt (their new assortments of bar chocolates are sinful) and Cailler in very good prices. The organic coop chocolates are very good too.
www.lindt.com and www.cailler.com
The MIGROS supermarket has its own assortment -Frey, cheaper but not as good or in such variations as Lindt and Cailler.
Sprüngli is famous in Zürich, his chocolates are excellent but expensive and it is more known for his Luxemburgeli (kind of tiny meringues with various cream fillings).
Then there is Teuscher (whose chocolate is -at my opinion- a good reason to migrate to switzerland) but also quite expensive.
www.spruengli.ch
www.teuscher.com
If I may say so: Migros if you like good chocolate, COOP if you like very good chocolate, Teuscher if you adore chocolate and Srüngli if you go for the best.
There is a chocolate train (in the area of Montreux):
swisstravelsystem.ch/…
which is worth doing if you have the time.
The Lindt factory is in Kilchberg (so near to Zürich), I think they do not make public tours but have a small museum.
The Cailler (Nestlé) factory is in BROC (near Fribourg ) and according to their site they offer tours.
To any of these places you can go by train and also enjoy the way there. Fribourg is also a very nice town to visit anyways.
hope this helped a bit
Tak