Thanks, Sam, and welcome!
Are any particular rivers/regions of interest?
I rode from Amsterdam to Vienna via the Rhine and Danube last Sept/Oct, and thoroughly enjoyed it all. In Austria, I met a group of seniors from Quebec who were on a "Bike and Boat" tour, riding from Passau to Vienna by bike, then going by boat from Vienna to Budapest and back by boat -- all in ten days. BUT, they were renting bikes from the tour company.
Saw lots of tour boats on both the Rhine & Danube, but none, so far as I could see, included people with their own bikes. (I found myself surfing tour-boat passengers on walkabouts in several spots -- no-one had bikes, that I could see.) So, I'd echo Andy's observation that the tour operators don't encourage BYOBike.
I did a quick search on Crazyguyonabike.com, looking for "Europe + bikes-&-boats" and that generated a
lot of journals -- one would have scan these to see what's offered. Here's the link:
https://www.crazyguyonabike.com/search/?query=Europe+%2B+bikes-on-boats&main_type=journals To augment what you learn from the Thorn forum, you might post a question to open a Crazyguy forum, and see what answers you get. (There's a
lot of info on Crazyguy -- sometimes it can be difficult to winnow through to find what you want.)
If you'd like to have a look at my journal from my trip last fall, here's the link:
http://www.crazyguyonabike.com/doc/2012Rhine-Danubetrip I did take a short trip on the Danube ferry between Weltenburg Abbey and Kelheim, to see the Danube Gorge -- that's a standard item on the Danube Cycle Way. There may be other local riverboats which take bikes, as well. Expect a Google search of German and Austrian Tourism-Office sites for those two rivers would turn up useful information.
I was camping about 2/3rds of the time, and that may not be to your taste; but the journal does give a good recap of the kind of cycling you're likely to encounter -- so several reviewers have told me, at any rate.
Good luck, in any case, and enjoy your new bikes!
John