We spent 3 weeks travelling around eastern Europe last May/June and made our way thru Croatia: I can say for certain that there is commercial rafting in Croatia but I don't have specific details.
We stayed at this place near Plitvice National Park in Croatia: Plitvice Mirić Inn
There were some brochures there for rafting and I made a casual inquiry: sounded like the better whitewater is across the border in Bosnia which is not too far from Plitvice. We weren't interested in rafting on that trip I was just curious.
I would recommend a visit to Plitvice and the place above is excellent for lodging and dinner. You could try contacting them for rafting info too.