Transportation options between Vienna and Budapest

Your best bet is simple--take a train.

We stopped in Bratislava and spent a weekend recharging our batteries. Then we took the 38 mile bus into Vienna--one of our favorite cities.

Then we took a train up to Prague.

If the Side Trip Tours sounds interesting and reasonable for you, I would do it Prague to Vienna and just take the train Vienna to Budapest (it’s only a 2 1/2 hr ride and €200 sounds excessive for that short trip). But that’s just an opinion and yours is as good as mine. Better, actually, since it’s your trip.

The rail line from Vienna to Budapest goes right thru Gyor. Gyor has an interesting old district that I enjoy more than Bratislava. Yes, it's smaller than Bratislava's old town, but not Disney-Like, as is Bratislsva's old town.

Gyor is about 1,25 hours out of Vienna. From the train station in Gyor, you can take a taxi to the Archabbey at Pannonhalma (google it). It's about a 30 min trip. Then a taxi to Gyor's old district for lunch and a look-see, then the train about 1,25 hours to Budapest.

I recently did this but in a different order.

Flew into Vienna, arriving around 9:00 and spent the day there. Took the 17:10 evening train to Prague and checked into my hotel by 21:00. Explored Prague for 3 days. Then took the Prague > Budapest sleeper train, leaving around 23:00 and arriving around 8:30 the next morning. Explored Budapest for 3 days. Then took the train from Budapest back to Vienna with a stopover in Bratislava. Explored Vienna and Bratislava for 4 days (they're only about an hour apart by train or river ferry), and flew home from Vienna.

While in Budapest, I booked a Danube sightseeing cruise with Legenda based on the RS guidebook (there's a special RS discount!); I would say Budapest from the river is a bit more interesting than Vienna from the river, especially at night.

Another option is fly to Vienna, then the train to Budapest, then a discount airline to Prague. Saves maybe 3 hours of travel time but adds nothing to the sightseeing.

I did a sleeper train a few days ago. Granted not the newest train or the newest tracks, but was the last time I will do that if I have any other option.

You can go between Vienna and Bratislava via the Danube. Then on to Budapest by train.

If you were to do:
Fly into Prague then Fly to Budapest, then train to Vienna, before October, i would suggest that you get a transfer service (i know one) from the airport to Szentendre, spend about 3, maybe 4 hours before taking the boat to Budapest [45 min]. I also know what to do with your luggage to make tis fun and easy. Rounding Margrit Islsnd and seeing the Hungarian Parliament seemingly rise up out of the water is a memorable experience.