Where to stay?

I would pick neither, but if I had to choose, it would be whichever is most convenient for transportation to your next destination.

Would you recommend staying in Geneva over these two?

No. None of these big cities give you the mountain experience that we consider to be the best aspect of Switzerland. Consider instead the Lauterbrunnen Valley, or Luzern, or Appenzell, which is closer to Germany. Since you are driving, you don't have to worry about the number of train connections that sometimes make Appenzell feel inconvenient.

jean,

If you want a city, I'd suggest Lucerne. If you don't mind something a bit more "rural", the Berner Oberland is a good choice.

Jean,

Is this a stopover on the drive to Fuessen, Germany? (The U with 2 dots can also be written this way). I'd suggest Appenzell or even Liechtenstein. While I wouldn't go out of my way to see Liechtenstein, but if you're passing close enough by anyway... We stayed in Triesenberg, Liechtenstein here:

http://www.hotel-oberland.li/

Paul