Café im Kunsthistorischen Museum dinner & OBB kombiticket

Traveling upstream the river Danube, i.e., from Krems to Melk, is slow and a waste of time. Given that you have only 3 days in Vienna you should consider whether it is worth to spend a full day for an excursion to the Wachau valley.

If you want to do it, to provide the sought train experience go by train to Krems (train REX 4, sit on the upper deck if available) and continue on the private Wachaubahn. The views will be the same as from a boat. If the weather is good I highly recommend to get off in Dürnstein. Take the adventure to climb the hill to the top where there are the remnants of the former medieval fortress (about half an hour). I guess the daring kids will love it standing on the very top of the rock. The view is breathtaking. After having explored the picturesque town you can continue to go to Melk, either directly by bus, or by Wachaubahn train to Emmersdorf and then by bus to Melk. The monastery in Melk is a world-class architectural and cultural landmark, but I have some doubts that the kids will really appreciate it. From Melk there are direct trains to Vienna.

If your kids are interested in railways consider a visit of the Museum of Technology. Besides all other exhibits there is a special exhibition on the occasion of "200 Years Railway".

Tickets for the Kunsthistorisches Museum are always required for entering, dinner or not. I assume that a table reservation is a must as early as possible. I guess if you have dinner then a guided tour is included.

I have posted extensively on a day trip to the Wachau. I recommend skipping the boat altogether and going by bicycle for some of the stretch between Melk and Krems. May would be lovely.

I've only ever had cake and coffee at the KHM cafe.

The Cafe at the Museum is beautiful. We had lunch there in 2019 and I don't remember what we had but it was good.

Agree that the Kunst cafe is good. As with most, have just been for lunch, but presumably dinner is the same. Looks like the museum is open late on Thursday so the cafe correspondingly is as well. I don't see any reason to think that a guided tour would be included, any more than it would be visiting the museum and eating at the cafe any other time. Question though is how much stamina the kids have for art that late in the day -- and would you be trying to see something of the museum before dinner, or after? Strategically, I think the highlights to focus on first for a family visit are the Bruegels, Bosch and Arcimboldo's four seasons -- kids will dig that! I've been twice to Vienna and still haven't made it to the Wachau Valley -- need to go back again! An alternative idea for a good day trip by train is Bratislava, about an hour away and an interesting city in a different country to look around for a few hours.

I don't see any reason to think that a guided tour would be included, ...

I do, because it is written here: https://www.genussimmuseum.at/dinner-at-the-museum/

The proposed schedule is:
6pm to 8pm: dinner
8pm to 9pm: guided tour (museum exhibitions close at 9pm)
9pm to 10pm: have a coffee, winding down the evening (restaurant closes at 10pm)

For the train journey. You have so little time in Vienna I wouldnt do it. BUT, if I had to I would look at somehting like going to St Pölten for lunch. Its a cute town, but someone may know one that is better, and its a 30 minute trip on the train, and the train departs Vienna Meidling which is a bit more interesting than Hbf and a lot easier and faster to navigate.

... the train departs Vienna Meidling which is a bit more interesting than Hbf and a lot easier and faster to navigate.

Trains to St. Pölten depart also from Wien Westbahnhof and Wien Hütteldorf when going by Westbahn, even more simpler train stations.

Being only 3 days in Vienna and spending one day in Wachau valley I would not waste time to go to a nice albeit provincial town like St. Pölten.