The best thing is, as already mentioned here, to check the train operator web sites: Check either the ÖBB links stated above or the Czech railways' web site (
https://old.cd.cz/en/default.htm). Be aware that ÖBB shows prices in Euro, while CD shows prices in Czech Crowns.
The Railjet trains used on the direct trains between Vienna and Prague can be bought on with both operator's, so you can just see which one is cheaper.
BTW: Remember that when you book a ticket on ÖBB you have to perform an additonal step to actually receive the printable PDF ticket (alternatively you can get a mobile ticket on your phone or a code for printing it at an ÖBB ticket machine, but you have to choose one of those three options).