<<"Are Murren, Wegen, Grindewald to out of the way to be a base?">>
I assume that you mean as a base for the trip to Lausanne?
Consult either the forum link to the time table ( which does not display the "via" option until you get into it), or the SBB home page.
You'll find that simply entering Grindelwald as a starting point and Lausanne as the destination will give you a 2 hr 51 minute journey via Bern.
The time table defaults to the fastest route.
If you choose the frequently recommended scenic "Golden Pass" route through the Simmental and down to Montreux through the vineyards, by entering Zweisimmen in the "via" menu box, you'll get 4 hrs 21 minutes.
You could decide on your tradeoffs.
<<"Would Bern, Thun, or other be better. I assume Lucerne is to far away if I want to spend sometime in Lausanne area.">
Use the timetable for a first check on various travel times. Since the alps seem to be your major focus, your base location should maximize your time there, it seems to me. Once you have travel times, you are well on your way to judge your tradeoffs.
Depending on what you want to do in Lausanne, you might consider taking the train from the airport to Lausanne on your first day, catching a nap in the first class car, where you have more legroom and likely fewer co-passengers. Then , stay in Lausanne the first night, or travel partway, such as to Montreux, or Bern....break up that segment, perhaps. Or take a late afternoon or evening ride to Grindelwald, Wengen, etc.
Zürich Flughafen to Lausanne - 2 hrs 27 minyes; twice per hour. Trains at xx13 do not require any change. The others seem to require a change at Bern. Restaurant car as far as Bern (or all the way if you take the one with no change of train.)
You'll need to keep in mind how you and your wife handle jet lag, if you choose this option. Of course, if you sleep through Lausanne, you can look at Geneva, instead. ;-). I fall asleep easily on the trains. ;-(
When you get to Lausanne, the (relatively) new Metro line down to Ouchy will impress you.
In early October you are beginning to start to sort of possibly get into the iffy time for snow on the highest trails near the Jungfrau. Usually, late October is problematic, and early October is OK. You are also beginning to get close to the start of the "between seasons" period. Some lifts to mountain tops or hotels may be closed for maintenance. Usually, that gets serious in November or December, not October. But, if you have something specific in mind, double check the availability. The time table can give you guidance. I have had wonderful weather in early October.
However, because thick clouds can take a way a lot of the impact of going up in the Alps, it's good to have at least a couple of days there to increase your chances of clear weather.
Everyone has there own preferences. I like Wengen: