I'm trying to figure out the best way to travel from Vienna to Prague. Some people have said train travel is more difficult because of luggage but it isn't a long trip.
There are also so many sites to find rail tickets with different prices. I don't want to book on a site that is not reputable.
Any advice?
The best way is by train. The trip is down a river and the scenery is mostly flat farmland. It is not particularly interesting, but it is an easy 3/hour trip.
The train is the way to go. City centre to city centre without all the hassle of getting to and from airports, check-in times and whatever.
Consult the trustworthy Man in Seat 61 for all details for this trip. When bought in advance tickets can be as cheap as EUR 25 per person. You can buy them with the Austrian (OEBB) or the Czech (CD) railways.
The best transportation is train. Little bit less than 4 hours. Scenery is mostly flat or rolling hills. Nice scenery is between Brno and Chocen - deep gorges, tunnels, wooded valleys with rivers. The train does not stop in Chocen. The best prices are usually here: http://www.cd.cz
If your luggage is large enough to dictate your mode of transport, then I think you need smaller luggage. Trains do have plenty of luggage space, which easily accommodates bags that are airline carry-on size, but there's no actual size restriction. You just have to be able to carry it on board yourself.