Also I'd give bratislava a miss. Eastern European cities do get pretty generic after a while, and that has neither the sights or the punting. Maybe stop for a day, but you're better off in Vienna for both tourism and punting.
Also, south of Slovenia is amazing for scenery but pretty dry for punting, so if you do decide to head down there, get your fill in Austria first (I once drove from halfway down Croatia, through Slovenia and into Austria for a punt and a McDonald's, then all the way back to Croatia to my hotel in Zagreb).