Geneva or Zurich?

Neither. Head to the Berner Oberland section of the Alps for three days: Interlaken, Lauterbrunnen, Murren, or Wengen.

If you must stay in a city head to Luzern. There are direct train to Basel from Interlaken, journey time 2 hours.

If you have 3 days in Switzerland, neither Zürich nor Geneva are good ideas. They are nice, but they are both cities, and what Switzerland is famous for is mountains.
Fly into wherever you can get cheapest and most convenient flights to: Geneva, Zürich or Basel. Then immediately get on a train to somewhere in the Alps, either Luzern or one of the places above Interlaken in the Berner Oberland (Grindelwald, Lauterbrunnen, Mürren etc.)

November won't be the best weather, summer is over, but it is not yet ski season, so it may be variable with rain or snow higher up. Luzern has trips on the lake, both places have trips up mountains (good weather only). If it is a total weather wash-out day, take a trip to Bern.

I agree with the other posters. With 3 days, Luzern or the Berner Oberland are where you want to be but ...

If you feel you must stay in one of these two cities then I'd choose Geneva. I'd take a 30 min train trip and actually stay in Lausanne. You could easily do a few day trips from there - Montreux, Chateau Chillon, Gruyeres, Lavaux Terraced Vineyards walk.

Consider Olten, it is one of the main switching points in the train system. And depending on the weather you can easily make day trips in any direction. Also because it is not a tourist trap, you should find that accommodation costs etc are much more favourable than other location in Switzerland.