Vienna Danube

The Danube was re-directed away from the city center of Vienna ages ago to prevent flooding. As a result, the Danube itself is quite far from the city center and few tourists make a trip out to see it. In addition, the river is industrial and not very pretty.

That said, if you really want to see the river, then you can easy take the subway line U1 and get off at the Donauinsel station. The Donauinsel (Danube Island) stop is situated on top of a very long skinny island now used for recreation. You could walk there, but it would take quite a long time and doesn't really seem like a good plan if your time is limited. The neighborhoods you'd pass through are also not attractive.

I'm sure you can rent e-bikes somewhere in Vienna, but I've never done it. I use the free city bikes which require some muscle.

I'm not quite sure what cities you are thinking of when you say "cities that the cruise ships stop at on the Danube." Do you mean Bratislava, Melk, Krems, the Wachau, Linz or something else?

You can take a train or car anywhere, of course. Some routes follow the river, some don't. You can easily look at Google Maps for this information.

The "Donauradweg" (Danube bike trail) runs along the river on its full length (1800 miles, 2850 km) through eight countries.
https://de.wikipedia.org/wiki/Donauradweg_(D6)

We took the U6 train to the Neue Donau station and walked on the north side of the river. It was a very pleasant green space day. People were playing in the water and in the parks along the path. Birds were singing, butterflies dancing. The photo we took of a park map is labeled Abschnitt 8, if that helps you find it.

Perhaps consider a day cruise to Bratislava. The Danube has been changed considerably with damming, especially so at the Iron Gates. Patrick Leigh Fermor's books give wonderful insight to all the changes (geographical, economical and cultural) to central Europe since the early 1930's. Wonderful travel books. That being said, the trains going west from Vienna somewhat follow the river up to Tulin but are on average a kilometer or so away. After that the train does not approach the river again until Melk, I think.Then it follows for a few miles before separating. Consider a train to Tulin or Melk then renting bikes for a bit? The distance between the two is 80km or so. With gentle pedaling and stopping for sites you should complete in 5-6 hours.

The most scenic railway is the "Wachaubahn" which runs through Wachau Valley along the Danube river.

You go by a regular train from Vienna to Krems first. The Wachaubahn operates between Krems and Emmersdorf, from where you may go by bus to Melk for visiting the Abbey.

https://www.wachaubahn.at/en

There are several companies offering bikes for rent. A very well known company is Nextbike which has bikes at various locations. You may pick up a bike at one location and drop it off at any other. That makes it very easy for one-way trips.
https://www.nextbike.at/en/
It is still winter now, and the summer season for bikes starts in April. So you won't find much places having bikes available now on their homepage.

A lot of people go to Melk by train or train/bus, visit the Abbey, pick up a bike, cross the river, and ride along the northern embankment of the Danube to Krems, passing all the cute little towns on their way.

wmt1 is right when it comes to train. Even better is rent a car or sign up for local guided tour from Vienna

Note: The S-bahn will get you to Krems.

There is no s-Bahn that goes to Krems from Vienna. What are you even talking about?

It is a REX train (regional express) from Vienna to Krems (a ride of 1:10 hours).

You might consider a view of the Danube from the Kahlenberg, or better yet from Weingut am Reisenberg with a glass of Gruener in your hand.

Having taken some 54 EU vacation trips, including about 23 to Austria, I am a confirmed believer in travel by car. From Vienna, drive along the scenic Wachau valley to Maria Tafrl pilgrimage church. Then to Melk. Return via Krems (and Durnstein if enough time).