The Vienna/Budapest Express we took did not cross into Slovakia.
There was passport checks leaving Austria ( but no stamps) and again entering Hungary (stamped) .

I would expect the hydrofoil to be more scenic, but despite suggestions there was no need to pre-reserve a seat for the train.
One other great advantage if you have a Ist class ticket you get entry into the nice First class lounge, free drinks and snacks in Vienna (also Salzburg).

mike