Jan 13, 2016 - 9:27 AM
Welcome to MySwissAlps moilam!
I would not recommend a flight for such short distances. Just make sure that you optimize your itinerary to end your stay in Switzerland closer to the Austrian border: so do not end your stay in Geneva, but in Zurich for example. The trains from there to Austria are comfortable, scenic and of course it's more eco-friendly than flying.
As for where to stay in Austria: this website is about Switzerland only, but if you provide more information about your expectations and interests someone might be able to help. Salzburg may make sense as it's closer: less than 5.5 hours by direct train from Zurich. It's a pleasant ride allowing you to see more of the Alps.