Its all a matter of preference. There isnt a right or wrong on this one. I like planes better than trains. I prefer moving around, drinking coffee in the airport (breakfast too) and I dont get worked up at the que to get on. I've done both the Vienna train station and the Vienna Airport on more than one ocassion so my opinion is not just in general.
The Vienna train station is quite an experience. Very much like an airport in many ways … and for good reason as millions go through it ever year. Figuring train station to and from times, the trip by train will take not less than 7 hours door to door. The first direct train is at 8:00am so you will be at your hotel not sooner than 3:00pm. The cost apparently is 30 euro. BUT, do check the cost with the Polish rail lines as OeBB tends not to have as many discounts as some of the other rail companies. Odd, but multiple companies sell the same seat on the same train for different amounts. You could reach the train station (both ends) with public transportation or if you have a lot of luggage and want the ease of a taxi, budget maybe 50 euro (just a guess) for the taxi.
“Trains are mass transit. No need to worry about train travel half a year in the future ...” but as you have invested tens of thousands of dollars in your holiday, and this is maybe a once in a lifetime experience you are not a typical mass transit commuter so do buy your ticket when it is first convenient to do so. Prices can go up and as the date becomes closer there are some rare occasions when seat selection becomes limited.
Some trains have wonderful views. These are usually marketed as such. That you will have to research, because the majority of trains I have been on in Europe have no views worth seeing. To keep noise down they buffer each side of the track with vegitation and when going through cities there are walls on both sides for noise control. I dont know about this trip. Out of the 6 hours you might get an hour or two of nice views, you might get a lot more, you might get none.
The Vienna airport is smaller and easier to navigate then most, so that’s a plus. Figuring all the time issues with a flight the trip by plane will take not less than 4 hours door to door. It almost seems like the Ryan Air flight is at a different time every day of the week. Some days you can leave early and have a full day in Krakow some days you leave late and spend the day in Vienna, rest up and hit Krakow in the morning. The flight with a checked bag will be 50 to 75 euro depending on the time of the flight. You could reach the airport with public transportation or if you have a lot of luggage and want the ease of a taxi, budget maybe 75 euro (just a guess) for the taxi.