I partially agree with Russ, don't bother with the Rhein boat upriver (south) of Bingen, but, IMO, the better part of the Rhein is between Bacharach and St. Goar. You get to see the Loreley, which actually is only a big cliff, but historical, the shoals where so many boats wrecked, and the Pfalzgrafenstein, the mid-river toll castle, up close. Other than Bacharach to St. Goar, the boat is too slow. Use the train to make the best use of your time.
The trip down (with the flow) the Rhein from Bacharach to St. Goar takes 40 min. The other way (against the flow) take 70 min. I made the mistake of taking the boat from St. Goar to Bacharach. I found the boat excruciatingly slow. We looked at the same part of the river forever. Forty minutes, IMO, is plenty of time on the boat.
Go with you luggage directly to Boppard. The next day, take the train to Bacharach, with maybe a short stop in Oberwesel. Tour Bacharach, then use your train ticket at the boat ticket kiosk for a 20% discount. Take the boat to St. Goar. Visit the Rheinfels castle ruin. If you have time, take the ferry across the river to St. Goarshausen and the train from there to Braubach and visit the Marksburg, the only Rhein castle never destroyed.
Or take the train back to Boppard and do the Marksburg the next day. I might do Boppard to Braubach on the boat. It only takes 30 min whereas the train through Koblenz take 45 - 60 minutes. And, the trolley that takes you up the hill to the Marksburg meets the boat at the dock. Coming back, you can take the train via Koblenz, or, as I did, take the train 7 minutes to Filsen, then walk about a km to the ferry that goes across the Rhein to Boppard. The walk from Filsen to the ferry is an easy one, albeit alongside the highway.