I'm not sure about the stairs, sorry. But, I wanted to make another suggestion about which company to use. If you are interested in just the river cruise part, and don't mind if it doesn't make stops, Vedettes du pont neuf looks like a good company, and you can print coupons before you leave. Or, if you know you're for sure going to do it, you can pay online a get a bigger discount (but you can still decide later what day you want to do it). It seems like the cheapest option anyway, and they have night cruises, which the batobus doesn't (at least in the fall; not sure about summer).
Remember, too, there are lots of stairs in the metro. You might want to familiarize yourself with the bus map if stairs will be a problem for you. Good luck with your knee!