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.