If your plans are tge three with no stops in between, there is a tgird and fourth, faster, options. 3rd: Prague to Budapest by discount airline then train to Vienna. 4th: same as 3rd in reverse.
Prague wiĺ be the most intense in crowds, Vienna in cost and Budapest in enjoyment (I get to have my opinion). So I would do Prague first to get it out of the way, then slow down.
The Budapest airport every year gets awards and it's simple to navigate. I went thru Vienna a few weeks ago and it was pretty okay as well. It's been too many years since Prague for me to comment, but I suspect they have found an efficient way to deal with the tourist crush.