VacationsToGo has a sister site for River cruises - no clue if it offers good last minute rates though. I've been getting some great fares via email from the river cruise companies themselves this year - some theories that bookings are down because Americans are scared to go to Europe (well, airfare isn't lower, so....Not sure I agree with that hypothesis ;-) I think supply just exploded and prices are still fairly high, so.....)
We did a Christmas market river cruise in 2014 that sold different segments - some were fairly short. We were on NUE-BSL but some started earlier (Vienna) and some boarded in the middle, so.....
There are some ships in the German market that do very short ones but I cannot remember the names (there are a couple of German locals who post in the Cruise Critic river cruises forum who give some great info on that sort of thing - though of course on that site you cannot mention travel agents, so....)