There is a better way to see the Wachau. Krems is nice, but definitely not the highlight and not where you want to spend a few hours.
Take the train to Melk from Vienna. Explore Melk for a bit. Get on the boat (either Brandner or DDSG), buying tickets right there on the spot. Get off the boat in Spitz, Weissenkirchen or Durnstein. Durnstein has the most to do/see (climb to the castle ruins where Richard Lionheart was held captive; have an apricot dumpling at this namesake hotel's terrace). Spitz and Weissenkirchen, however, are more "real" and have better dining options. Whatever town you choose (maybe two, even), take the WL1 bus back to the Krems train station when you are done. These are small towns and the bus stops are obvious. You buy the ticket from the driver and it takes about 15 minutes from Durnstein to the Krems train station. It is a lovely day out when the weather is nice.
I prefer, however, to rent bikes instead of the boat. Nextbike has locations in all these villages where you can rent, if that is your thing. If you are in Vienna in April/May, it is very nice to see the blooming apricot trees. See can do this best from the bank opposite of Durnstein in the village of Rossatz. To get there, you take the WL2 bus from Melk.