It really is 6 of one and a half dozen of the other.
You get a free ticket for all public transport in Geneva from your hotel.
So if you stay at the airport (there are a few hotels that are more or less
walkable from the terminal), it's easy and fast to get downtown and you are
right there for your flight.
But as noted already, there are plenty of hotels right at Cornavin (main
downtown station), and getting to the airport is trivial. And the area around
the station is just fine, unlike some other cities.
Airport hotels are likely to be less expensive than downtown Geneva hotels,
might be one consideration.