The main outfits in Switzerland are either Alpin Raft or Outdoor Interlaken for the Berner Oberland or Swissraft out in the Engadine (Inn River). There are lots of cool rivers, but the rafting leaves a lot to be desired. That said, there's some money to be made if you're keen. If you're a kayaker, your best bet is to guide out of Interlaken on the Schwarze Lutschine, and get your runs in on the Weisse Lutschine, a real nice alpine IV-V run. The other rafting sections run commercially are the Simme (kind of lame...sorry don't mean to be negative) and the Inn (which has much better kayaking sections above and below).
Your best bet for kayaking in Switzerland is around Graubunden on the tribs of the Rhine or down in Tessin which is a creek boating paradise.
If you want to guide look at going either to the Embrum area in France or better yet, Austria around Pfund. Good luck.