...my wife is worried if she can actually sleep (2nd class sleeper) on the train because of the noise
Well,
Czech sleeper carriages (used on route from Prague to Krakow) and especially
Polish ones (Krakow to Budapest) aren't that bad, so noise shouldn't be a problem unless next compartment will be occupied by a bunch of teenagers or football fans. Otherwise usually passengers tend to complain more about some wavering during the ride (though it's not throughout the whole route & some even consider it helpful to falling asleep)
we thought about flight Prague - Krakow - Budapest, but the flights are not direct (some take longer than train!!!!) and still very expensive
Yep, sometimes it can be a problem to fly between the Central European cities. Not that long ago used to be cheap RyanAir flight from Krakow to Budapest, but apparently it's canceled and now only Warsaw-Budapest is offered by both RyanAir & Wizz Air. Although in some cases it might actually make sense to catch a train from Krakow to Warsaw and fly from there, especially since it's a problem to purchase cheap train tickets form Poland to Hungary. Will be quite a detour, but after all it can be cheaper and faster. Also there is bus option from Krakow to Budapest, unlike train buses go via direct route, so travel time is considerably less compared to rail connections. While with Prague to Krakow it's more or less either daytime or overnight train options
Another question is the fares for each leg of the journey, ie. (1) Prague - Krakow, (2) Krakow - Budapest, (3) Budapest - Vienna.
Ok, so full fare one way train ticket Prague-Krakow is 41,6 euro + sleeper reservation 21 euro (double), Krakow to Budapest is 82,8 euro + 21 euro for double sleeper & Budapest to Vienna is 22-25 euro (depending on train). Paying full fares for the above trips is a bit too much, it's Central Europe... that is why there are quite a few tricks on how to travel cheaper. Easiest trick is with Budapest-Vienna route, because here it's possible to purchase discounted 13 euro tickets, should be bought in advance via MAV website (guide on how to do it
http://europetrainsguide.com/Advice/How-to-Buy-Train-Tickets/Hungary-MAV.html). More complicated things is with Prague to Krakow and Krakow to Budapest. For the later there are available discounted tickets (only 49 euro for ticket+reservation in double sleeper), but the problem is that currently Polish Railways (PKP) doesn't sell such discounted tickets online, while purchasing it in Poland yourself won't really work, since it will be too late (discounted tickets sold in limited amount per departure). So what you can actually do here? Our suggestion will be to take advantage of some tariff nuances, because main point with Prague-Krakow and Krakow-Budapest trips is that leg Bohumin-Krakow is shared by both. As result to bring down the price it is possible to purchase three tickets instead of two, meaning first to buy domestic Czech ticket Prague-Bohumin (from 310 CZK per person or even cheaper with 2> traveling), then at the same time you also purchase return ticket Bohumin-Krakow-Bohumin (22,4 euro per person) and one through sleeper reservation Prague-Krakow. Return part of the ticket Bohumin-Krakow-Bohumin will be used for trip from Krakow to Budapest. In order not to buy missing ticket Bohumin-Budapest on the way back it's also possible to buy it in Prague even before journey to Poland (will be 51,4 euro per person). While in Poland just purchase one through reservation Krakow-Budapest. General idea here will be to save while having three tickets (Prague-Bohumin one way, Bohumin-Krakow return & Bohumin-Budapest one way), but only two sleeper reservations (Prague-Krakow & Krakow-Budapest) for direct overnight trains. Such ticket trick is totally legal and relatively easy to do, as result it will save you out of nothing 40+ euro per person. It's possible to bring the price down even more, but then itinerary will be slightly complicated and involve train change
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