If you are arriving at Geneva airport and going to Annecy it is better to use the main exit on the Swiss side (there is a French side of the airport in Ferney but it is the opposite way from us).
Different ways to go to Annecy:
1/ By train
When arriving at the airport (main arrival terminal), just follow the sign CFF train station (same floor), you will then find Cointrin train station: you have 5 trains per hour going to Cornavin station (Geneva center) there you will find trains going to France.
It will cost approximately 20€ but will nearly take 3 hours, not easy if you have lots of luggages, travelling with kids, arriving at night or on Sunday and better to have Swiss Francs...
But if you do not have much luggage and some time, you can stop in Cornavin to visit Geneva center before going to Annecy.
Find below websites:
2/ By bus
The company "Frossard" offers a regular service to take you to Annecy.
It will cost approximately 10€ one way, it will take nearly 2 hours (Geneva airport/Geneva center/Geneva Unimail/Motorway)
But faster to do Annecy/Geneva airport as direct with motorway.
But not so many buses per day and in case of flight delay it can be long to catch the next one, also difficult if your flight is arriving late evening.
3/ By taxi
I will not recommend you to use the Swiss taxis are they are double price than the French ones.
To save you some waiting and to follow taxi regulations please book your French taxi in advance. Depending on arrival times and taxi companies, it will cost from 90€ to 140€ for a taxi from Geneva airport to Annecy.
Using a taxi is the fastest way, flexible and easy but more epensive.
I will be happy to give you a free quote on http://www.taxi-massingy.fr/