Not only is the train a great way to get around, but there are a few cruise lines and ferries that run on the Rhine river between Koln and Frankfurt. I took cruise with the KD (Koln-Dusseldorf) line company, and it was great. They run cruises all throughout the year and at several times every day. You can simply go to any town on the Rhine River (Germany of course), and go towards the water or port. You'll easily be able to spot the big KD-line dock and ticket booths where you can buy tickets for the days trip. If you have a Eurail pass, just show them at the ticket booth and you get a free ticket!!!!
KD also does cruises around Europe, and you can check out prices, timetables, info, etc all at their website on http://www.rivercruises.com/.
Do note that Cruise line do not run in Winter or are limited to boring tea time cruise.
Do check if the cruise are running if you are planning for a Rhine Cruise to visit the Rhine River castle and sights in Winters