With 5-6 days you'll of course want to focus on towns, castles and activities in the Upper Middle Rhine Valley (between Koblenz and Rüdesheim anyway) on both sides of the river. Braubach and Bacharach have some extra-nice old half-timbered buildings. Be sure to tour Marksburg Castle in Braubach. A good cruise begins either in Bingen or Rüdesheim, near the southern end of this area, and ends either in St. Goar/St. Goarshausen (which lie across the Rhine from each other) OR in Boppard (north of St Goar, cool chairlift ride there.)
Train lines run along both river banks through the UMRV. Because St Goar is centrally located there, because St. Goar has a ferry crossing which sets you up for catching a train along the east bank, and because it lies in the most scenic zone of the UMRV and offers hotel rooms with extra-nice views, it is a great place to book a room for perhaps 3 nights. From the St Goar train station, you're just 10 minutes from Bacharach, 5 minutes from Oberwesel, and 10 minutes from Boppard, all of which are fellow west bank towns that share the same railway with St Goar. I'd look into the Hotel Rheinfels and the Rheinhotel St Goar there - they are right next to each other facing the K-D cruise boat dock and the river, only a 2-minute walk from the St Goar train station.
I would consider also 2-3 nights on the MOSEL River, the little-sister tributary of the Rhine which terminates in Koblenz. It's a very pretty and interesting river valley as well, one with a somewhat different vibe from the Rhine. Cochem is a central and very attractive base town for train travel along this river; nearby destinations include Trier, Burg Eltz (tour this castle too) and Beilstein (a 1-hr boat cruise from Cochem.)
You don't say when this trip is. That matters a lot if you wish to hike/bike/cruise and take gondola/chairlift rides.
Koblenz may be worth visiting too, but it's not one of those small adorable villages - it's a mostly modern city with a few attractions. It will no doubt be a place where you change trains a few times, as both the west and east bank train lines on the Rhine meet up there - and the Mosel River train line does too.