Six days in Switzerland is better than no days there. It is enough time to make a nice journey across Switzerland to meet your flight home in Geneva.
Your son will travel for free on a Family Card which you request with whatever pass or card you buy. Munich card or pass is best depends on the route you choose. We like the 3- day Flex Pass but you would have to run the numbers to see what is most cost-effective for the route you choose.
The main direct train from Innsbruck takes you to Zurich but do not stop there. I am going to suggest a nice "Switzerland sampler" that includes some special places that should appeal to you and your son, if you want to experience more than the tourist's Switzerland.
Day 1 continue from Zurichnthe short distance to Arth-Goldau. The total journey time from Innsbruck to A-G is 4.5 hours. There you change to a cogwheel train that climbs up Rigi. Go up and over the top and down to Rigi Kaltbad. There is a nice selection of hotels there and fabulous walks with views over the lake ( commonly called Lake Lucerne although that is not the true name).
Next morning ride the cablecar down to the lake level at Weggis and catch a boat to Lucerne. Stash your bags in a locker and spend a few hours exploring the town,then continue on to the Berner Oberland for the next three nights. I suggest Mürren and specifically chalet Fontana ( budget option) of Hotel Alpina. Then take the train westward as far as Spiez and transfer to Kandersteg, a short distance south. At Kandersteg, store your main luggage in a locker and pack your overnight needs in a daypack or whatever you have. Walk through town and catch the lift up to Oeschinensee, an incredibly beautiful glacial lake situated well above town, surrounded by cliffs and peaks. Bood a twin room at the rustic mountain inn right on the lakeshore, Hotel Oeschinensee.
Www.oeschinensee.ch
The inn is rustic, with bathrooms down the hall, but everything is sparking clean, and the location is amazing. So is the food served at dinner from the family's organic farm. This is one of our two favorite places in Switzerland.
On your last day your will return to Spiez and follow the scenic Golden Pass route to Montreux, where you can visit Chateau de Chillon if you are so inclined. Then make your way along the lake to a town near enough Geneva that you can make your 9 am flight. Mother trains start running pretty early but you might want to be within 30-40 minutes of the airport ( trains go right into the airport so no transfers need be involved). We chose Morges for this purpose, but there are other towns along the lake that would work as well.
