3-4 full days before a river cruise

Selkie, last question first.
Train is the obvious way to travel in Switzerland, there isn't anywhere in Switzerland that can't be reached by train (sometimes with connecting bus), and most towns an cities ban cars in the centre.
Look at the rail map of Switzerland here: https://www.sbb.ch/content/dam/sbb/de/infotexte/uebersichtskarte-sts.pdf
Each red line is a rail line with at least one train per hour. You can see Zürich airport (Zürich Flughafen) top right of centre, Basel top left. If you draw a line Geneva - Lausanne - Thun (south of Bern) - Luzern - St Gallen; everything south of that line is the Alps, everything north of that line is the "Swiss Plain" where most people live.

Airport - If you are coming from outside Europe, the obvious choice is Zürich or Geneva. Both airports are also rail hubs so you can get anywhere in Switzerland from them. Basel airport has lots of flights to other European destinations (and north Africa), but no intercontinental routes.

Where to go - You say "3-4 full days", it is better to count nights. I will assume 4 nights.
I suggest Luzern for 2-3 nights. Others will recommend the Jungfrau region (Berner Oberland), but Luzern is nearer and will give you a good introduction to Switzerland. It is a nice old town, on a lake, with three mountains you can go up by train/cable car.
Zürich airport to Luzern is only 70 minutes by train.
360° panorama of Luzern: http://tour.luzern.com/360/en/
You can take boat trips on the lake, which is large, and spectacularly fjord-like at the far end.
The mountains you can take trips up are Pilatus, Rigi and Titlis. Titlis is the largest and has a permanent Glacier on top. See here: https://titlis.ch/en

It is 75 minutes from Luzern to Basel by train; so unless your ship leaves very early you can get there on the day. You would then need to take a tram or taxi (expensive) to wherever your ship is docked.
I would recommend staying one night in Basel. There is a lot to see in this city.

Edit: Museums in Basel - see here: http://www.museenbasel.ch/en/museumsa-z/
Basel also is very pretty for just wandering around the old town.

Thanks! Lucerne seems to make sense- a pleasant place we can relax and recreate for a couple days before a cruise that has us moving all around the place. (I'm willing to put together some fairly complex routings on my own, but it's going to be a marathon trip rather than s sprint, and as a runner, I learned long ago to not start the 'race' at too quick of a pace, lest there be misery from the halfway point onward.)

I've only been as far as Luzerne, but many fans of our host's books feel that "Switzerland proper" begins farther away, in the Berner Oberland: https://www.ricksteves.com/europe/switzerland/berner-oberland . But for the time frame you gave, Luzerne (especially if you have time to stay in a lakeside village, instead of Luzerne (a nice city). We stayed at a very expensive hotel in Vitznau (there are two of those ... ) because you can walk to the cog railway for the adjacent mountain (we came down the cable car, and for lack of a public bus appearing, walked back to Vitznau.) Note that weather at the top can be foggy and disappointing, so check the summit-camera if you have time to go the next day instead. We also had a car to scout around the lake.

But one of the real plusses of Luzerne is that you don't need a car. The city is a rich destination, and there are lots of boats on the lake.

Since you mentioned architecture, check out photos of Stein am Rhein, Aarau, Augusta Raurica, and the Vitra Design Museum/Architecture Campus. For modern art, the Fondation Beyeler might be more famous than the museums in Luzerne. You might decide to spend the three days driving from Zurich to Basel. The Rheinfall isn't unforgettable, but is worth a stop.

Ditto Luzern. I'm not sure of your home town. But for me, oddly enough, Basel was the cheapest airport to use. I flew via Paris with Delta/AirFrance. When I've checked, Geneva and Zurich from my airport have been quite expensive relative to other European destinations. For something like a cruise, I'd like to sleep in the starting point, night before. My guess is that a train issue in Switzerland especially at that time of year would be highly unusual, but you never know. And Basel is a delightful town. We stayed at Motel One which is new and spotless. If you do have four nights, I would suggest three in Luzern and one in Basel.

I've been eyeing he Basel Motel One since the cruise came up because it seems like a good price/value point. Nice to have a datapoint that early perceptions are correct.

Selkie, usually I try to stay at places with some local charm, but Motel One was such a good price and quite nice. I would say the staff had local charm.

Your cruise probably won't leave till evening, so you'd be safe taking the train up on that day. We went on a B-to-A river cruise in July; we arrived in Basel from Luzern at around noon, and had tons of time to explore the town before the 9 pm departure. There's a train from Luzern every hour so it's easy to get there.

Enjoy!