I am planning an afternoon cruise up the Rhine from St. Goar to Bacharach and I not sure which boats travel the route and their schedule.
According to page 13 of this: http://www.k-d.de/fileadmin/user_upload/redaktion/Linienfahrten/Dokumente/KD%20Fahrplan%202011%20intern%20low.pdf the afternoon departures from St Goar are at 2:20, 3:20, and 5:20 and arrive at Bacharach an hour and ten minutes later. K-D seems to be the most popular outfit, but I've seen other docks and boats on the river.
Are you going back on the train to St. Goar after the cruise? If so, unless you just want to get your money's worth by spending as much time on the boat as possible, I suggest you take the train to Bacharach and come back on the boat. Because of the strength of the current, the trip down the Rhein (from Bacharach to St. Goar) takes only 40 min (½ hr less). That still gives you plenty of time to see what there is to see. I made the mistake of doing St. Goar to Bacharach, and the slow trip was excruciatingly boring.
We're traveling by train starting in Amsterdam and ending in Montreux Switzerland. I thought taking the boat from St. goar to Bacharach might be a nice change. We're heading from Bacharach to Luzern and I haven't yet figured out the best way by train.