Lake Luzern, Lake Constance, Brienz, Thun cruise - calm waters?

Yes, it does get choppy, but not very often. There is a wind called the Föhn. The Alps are high enough to have different weather both sides. When you get high pressure south of the Alps and low pressure north the difference causes strong warm winds to blast through the passes (being the only gaps in the mountains it can get through) down the valleys and cause turbulence on the lakes.
This is luckily very rare, like one or two days per month. Otherwise the lakes are totally placid.

Conclusion: It will be very unlikely to be choppy, usually totally flat. If there is a Föhn, just make your boat trip a different day.

Useless fact: In Switzerland, a hair dryer is also known as a "Föhn", named after the wind.

You probably won't know the conditions until the day and hour you get there. Just make decisions then and there.

The Bodensee - Lake Constance - has enough traffic on it that you get an occasional wake as a boat passes nearby, but it will be very little noticed - the passenger ships are pretty big to spread out the impact.

I have never noticed anything at all even a little on any of the other three lakes you mention. Very very smooth, unless the weather is bad, in which case you won't get on the boat in the first place.

Boats on the Swiss Lakes have frequent stops and in the unlikely case your partner feels really bad, you can disembark in the next port and take a train or bus back.

Unfortunately most of the stops on lakes Thun and Brienz have no train service and buses may be quite difficult - Giessbach as a typical example.

Thank you very much, Chris, Nigel, Stan, Marduk, for taking the time to answer my question. Chris and Nigel, thanks for your explanation of how a turbulence can be triggered. And, Chris, thanks for the bonus bit of information about another meaning for "Föhn".

Stan, you're right; we'll have to decide whether to get on a boat right then and there. And when the boat ride becomes uncomfortable, then we'll just disembark, as Marduk suggests. And if this happens on Lake Thun or Brienz, as Nigel tells me, we'll just have to walk all the way to where someone can give us a ride to the next bus or train pick-up point.

"And if this happens on Lake Thun or Brienz, as Nigel tells me, we'll just have to walk all the way to where someone can give us a ride to the next bus or train pick-up point."

You'd better just hold on till the next port with a train station. I can't imagine someone feeling that bad the he has to disembark immediately. Seasickness is part of the great adventure of mankind. Just imagine how many of those famous exploreres and their crew must have vomited their way onto the pages of history. Every hero has a human side as well. Imagine Columbus throwing up(or rather down) from the Santa Maria! So your partner shouldn't be ashamed if he has to "feed the fish". :-)

http://www.motion-sickness-guru.com/a-brief-history-of-motion-sickness.html

Marduk, OK; I won't rush to get off the boat when the undesirable thing happens.