Geneva or Zurich?

My suggestion would be neither. Have you considered spending the remainder of your time in Lucerne? It's a much nicer choice, and you can easily get from there to the Zürich airport in an hour or so.

So you don't think Zurich or Geneva have much to offer? Lucerne seems nice for sure, any specific suggestions?

If you look at Rick's guidebook (which I would hope you would do), there is no chapter on Geneva. At first I thought for sure I got a misprint, but not if you read the book he says don't bother with Geneva, do Lausaunne instead. Or Montreux. You can do Chillon from there.

I'm thinking that flight-wise, you'll have much more choice from Zurich and it's a nice sized walkable city. The airport is a really short train ride from the central station and there are several hotels right there if you want to simplify your departure.

Just because Rick doesn't include it in a guidebook, doesn't mean a town is not worth visiting. Rick has a limited number of pages and relies on his personal opinions about which places to include and which ones to leave out. There are so many places in Europe he simply doesn't have the time to visit or include in his books.
I personally love Geneva! It's a beautiful, cosmopolitan city on the shores of the lake with plenty to see and do. The views across the lake to the French Alps is stunning. The old town and it's gorgeous cathedral are well worth a visit. The cathedral has been excavated underneath down to the 1st century - it's pretty amazing what they have unearthed down there that you can walk through. Tons of antiquarian art and book stores and restaurants in the old town. The shoreline is lovely as well. If you're interested in science you can try to get a spot on one of the coveted tours of CERN - we did that a few years ago and it was amazing.
Gruyere is a great place and well worth visiting - if you are a fan of Alien then definitaly go the the museum and then to the bar across the street done in the spirit of the movie...uber cool. There is a nice chateau on the hill and the town itself is very quaint and Swiss.
Besides Geneva and Gruyere you can also visit Lausanne and it's beautiful cathedral and Chateaux Chillon in Montreux.

Having been to all the mentioned cities I too would echo Anita's sentiments. I like Geneva for its banking and church history, proximity to the lake and excursions around the lake, many international organizations (I've been to CERN also even going underground and walking over the super collider in between experiments), museums, beautiful old town, etc.

I highly recommend a day trip to Gruyere and the Geiger museum, castle and cheese caves. Broc is also nearby and they have a great chocolate museum and tour. For my 2 cents worth, I prefer Geneva to Zurich.

I very much vote for staying in Lucerne and flying home from Zurich. Geneva is just not at all what a quintessential "Swiss" destination should be.

Stay in Luzern instead. I say this because if you haven't done it then it is worth it.

If this is your Nth trip then check out a 'city'. I have found that cities around the world are more similar than not while their countrysides span the spectrum of what is possible to what is acceptable sometimes.

If you decide to do ZRH there is a great late night haunt moved whole clothe from Ireland...

That being said, the last time I stayed in Geneva I ate some great French food--in France ;) and slept in Geneva. Seriously, and then I stopped in Arbois (Jean-Paul Jenet, oh my goodness good and two Michelin stars) before heading back to Geneva. Geneva was nice but I am typically not a fan of busy and crowded and it was both. It was OK but so much more expensive than France across the border. I don't actually dislike it like I do the Charles de Gaulle airport or anything. I will probably stop back through it next time for some reasons (CERN among them).

BTW, yes Rick's books reflect his personal point of view. That's why he puts his name on the cover.

He admits they're not encyclopedic, but when he chooses one place over another he explains why so you can decide whether to follow him or not. It's not required, really.

The 2 F books tend to cover every single hamlet and village in every country.