Personally, I would take the Glacier Express over Zurich any day.

As for cheap hotels, they are not too common in Switzerland. For that price, you may be able to get a private room in a backpacker hostel, you can find those on backpacker.ch. The other source of cheap hotels that I know is "velotels". They are hotels that are quite basic and are designed with the bike tourer in mind (hence the word 'velo' in the name), but they also accept all other kinds of travellers, you can find a list of them on velotel.ch (unfortunately, only in German).

Somewhat central to all of the places that you listed might be Lake Thun / Thunersee: in the towns of Thun, Spiez, or Interlaken. However, it would be challenging to visit all of those places and to return to the same location every night, I might consider staying in a couple of different places during your trip.