From where I live both main Swiss airports are at about equal distance so I usually leave from Zürich since in the past most flights went from Geneva to Zürich before going where the went anyway.
This is however no longer true so now it is more a question of train schedules and airlines.Regardless, either way the trip starts with a small train down the mountain for 35 – 40 minutes before changing to a normal one which goes directly to the airport.