Marksburg was wonderful. My favorite, with Burg Elz coming in second. We opted not to take a Rhine cruise and were glad we didnt. It seemed like too much time floating, looking at things from a distance. Instead, we rented bikes (we were staying in Bacharach, and rented bikes from a local person whom our b&b hostess recommended) and rode along the paved, flat well established bike paths (which we also did along the Mosel, renting from bike shop in Cochem). A ferry crosses the Rhine quickly and easily, and the train runs along the Marksburg side, so between the three we had easy transport throughout the region that kept us up close and personal with places along the way. That said, we are younger than RS' average (I was 46 at the time and my daughter 13), and are avid bicycle riders, so a cruise could be a nice break in the site seeing and offer perspective of the whole before you conquer the parts. A half day seems like more than you may need though. I believe there is a 90 minute ride from Bingen to St Goar?
In the Mosel region, we took the train from Cochem to the station at the base of the hike to Burg Elz that RS describes. We then did the ~90 minute walk, part paved/part trail, and it was wonderful. Beautiful scenery, great way to emerge from the trail upon the castle on high. There is a nice cafe at the castle where we had lunch after the tour, and then walked back. I found Burg Elz to be more formal, like a museum, and more preserved in a cleaned-up and prepared for visitors way. Marksburg spurred my imaginings more of what it might have been like to live there back when.
the Rhine and Mosel are quite different and make for a nice contrast. Enjoy