I thought I'd add on a comment since we took our trip and took Emily's advice. We left Salzburg and went straight to Vienna. On one of our days there, we took advantage of the package deal from the train station to travel to Melk, saw the Abbey, and took the boat to Krems. While my wife and I each had a backpack and carryon only, it would have been really inconvenient to drag it all through the town and up the hill to the Abbey. Once there, I am not sure they have a spot for luggage anyway. I notice you do not mention the Abbey, but my own opinion is I rank that over the boat trip. The boat trip was also nice, the weather was perfect and the day enjoyable. I am sure you could get a carry-on and backpack on the boat, but you might find it a bit crowded on top deck for all of it and might not get a seat there, which is advisable because the viewing is better up there. Once off the boat in Krems it's a bit of a walk to the train station. I suggest re-doing your schedule to stay an extra night in Vienna and use that day to do the OeBB train deal to see the Abbey and boat trip without the luggage. While aggressive, I think you can still squeeze in Salzburg and return to Vienna for the flight home, but personally I agree with hlaufenberg, go to Salzburg next time.