On paper the car is quickest at around 3h30, but that assumes clear roads and ignores parking a car you do not need inside Prague. The coach is the cheapest way across, from about $15, and takes a similar four hours or so — but you trade the train's space, café and step-off-in-the-centre convenience for those savings. For a four-hour city-to-city trip, the Vienna to Prague train is the easy default.
A few travellers still consider flying Vienna to Prague, but there is rarely a convenient direct flight on such a short hop, and once you add getting to the airport, security and the transfer into the city at the other end, the plane saves no time over the train. The bus is the true budget option and can dip below the cheapest train fare, yet you trade comfort and a little speed for those savings. For the balance of price, comfort and city-centre convenience, the train is the option most people are happiest with.