I'm from Switzerland as well, live in Zug but work in Lucerne. I know some fabric, yarn and craft shops here and will list them:
aarlan (upper floor of the Vögele) yarn, wool and supplies
Alja Nouveau (fabric and supplies) a bit further than the Coop in direction of the Spreuerbrücke, sometimes it has some cute designs and there's a table with fabric for sale where you pay about half the original price and there's a remnant box as well
Vonarburg Voco AG (wool, yarn and supplies for knitting and crocheting in the lower floor, beads and other craft supplies in the first floor, fabrics in the second and third floor - in the third floor is Fasnacht-fabric, I've never been in this floor) it's quite expensive, but sometimes you can get good deals with remnants
Bead Box (a lot of beads, some are quite cheap, others are more expensive - depends on the material they're made of) I think they offer some workshops as well
There is a fabric store in the Neustadt, near Helvetiaplatz, but I don't know its name and it's very expensive anyway. There's another fabric store I've never been in the Neustadt. As far as I have seen, they sell very expensive and exclusive fabric like silk and so.
Manor has some yarn and wool as well as beads and other craft supplies like knitting needles, crochet hooks, zippers and so on.
There's an Alja Nouveau in Zug as well, down the train station in direction of the lake and then turn right, next to the Pickwick Pub. Another fabric store is in the Baarerstrasse 60. It's really small but has some nice fabrics sometimes. There are one or two other stores but I've never been there.
I was once in a big fabric store in Bern, near the train station. You had to go in the lower floors, the had a lot of other crafting supplies as well. Can ask a friend if she could give a better description. Oh, and I think in the Loeb you should get some fabric and craft supplies as well.
There's one online store I order from sometimes. It's called cotton-colour and sells mostly patchwork fabric. I don't like all they have but if you browse the fabrics, you can find some cute designs sometimes.
I think that's all for now... Hehe...