Are you thinking about staying in Switzerland, or would you like to go farther afield?
In the 10 years we have been here, we have been all over Switzerland and a fair bit of Europe with our dogs. I've found that many hotels, even if not listed as 'dogs welcome' will accept your dog if you stress how well behaved and quiet he/she is. Oddly enough, I've rarely had a problem with more upscale hotels - the problems I've encountered have been with 1 or 2 star hotels. I've had very good luck with small Gasthauser or Berghotels, especially family run ones.
With 1 dog, I never had any problems finding a welcoming hotel. With 2, it was still pretty easy. I've found more than two to be tricky, though. Nowadays I don't even try to find a hotel accepting of my crew - I opt for day trips, or rent a free-standing chalet.
(I no longer holiday in cantons enforcing BSL (like VS), so I don't know how - or if - tolerance levels there may have changed in the last few years.)
To plan a hiking trip in Switzerland, we like the Kummerly and Frey hiking guides (Wanderbücher). These are great little books, printed by region, with suggestions for day hikes and longer trips. (Available at most stationary stores and booksellers.) They give good description of the walk including timing, elevation changes, difficulty level, restaurants, overnight accommodation, points of interest along the way, travel directions, parking possibilities or public transportation info. These have been very helpful in trying to match the hike to my guys' abilities - and mine.
FYI, from Hundeweb, here is a list of dog friendly hotels:
http://www.hundeweb.org/pid/120.html
But, for 3-4 day trip you could pretty much go anywhere in Switzerland - with a bit more info as to your plans/interests, I could give you some specific suggestions.