Switzerland by train

It really depends on what you want to do. Be aware that some of the gondolas close at this time of year for the season, or for maintenance before the ski season. You might get some snow at higher elevations.

Many of the lifts start closing down around mid-October. Also, some lodging closes as it's off season between summer and ski season. Not knowing your itinerary, it's not possible to determine how this will affect your trip. It all depends on how much time you will be spending in the mountains. Obviously, the cities are not affected.
The first weeks of October would be better.
Hope you can enjoy this beautiful country.

And sometimes the weather begins to get rainy and windy by mid-October.

you could reach out to Railbookers to get their take on weather