I am interested in booking a riverboat passage from Frankfurt to Cologne. Are there any company's that one would recommend? How was your experience?

The only excursion boats I know of ply the Rhein and Mosel. If you go over to Mainz (about a half-hour from Frankfurt by train), you can check out the k-d.com offerings.

But I wouldn't go all the way downstream to Köln. The most scenic part of the river is between Mainz and Koblenz - the rest is mostly industrial areas and docks.