Hi,
You can do both. Have a look at this
Rhine, Main & Danube River Cruises
You can start in Amsterdam and then follow the Rhine River into the Rhein-Main-Donau Kanal entering the Donau at Regensburg and then go on to Vienna or even further to Bratislava and Budapest. The above link should give you a good overview of what you can visit. There are shorter tours that just do the Rhine river and there are others that go from Frankfurt through the canal into the Danube to Vienna and beyond.
We know the area very well since we have biked from Nuernberg to Vienna and back and also along the Rhine River.
Good luck. Let me know if you have further questions and I will try to answer them.