Burg Eltz and Marksburg in the same day?

I've never been to Burg Eltz so I'm not the one to advise you as to how long to spend there.

I have been to the Marksburg, so I am familiar with that end of your proposed trip. When I was at the Marksburg, I had lunch in Braubach and then walked up the foot path to the castle. From town, it looks like a formidable walk up a hill, so I was surprised at how little time it took. Google Maps says 21 minutes from the station to the castle, walking, and I'm inclined to believe it, maybe less time if you're fit. The Bahn website claims there is also a bus from the station to a cemetery, from which it is an 11 minute walk to the castle. The bus probably leaves the station shortly after the train arrives. Trains from Koblez are scheduled to arrive at 5 minutes past the hour. If you arrive at 15:05, you should have plenty of time to get to the castle in time for the 16:00 English tour.

The train connections that get to Braubach at 15:05 leaves Hatzenport at 14:05,. Look like you've seen the Burg Eltz to Hatzenport bus schedule. After 12:22, there are two buses an hour and there is a bus from Burg Eltz at 13:22 getting you to the Hatzenport station at about 13:45, twenty minutes before the train to Braubach leaves.

There is a change of trains in Koblenz. Looks like it is a cross-platform change in 16 minutes.

You can only be inside Burg Eltz with a tour, and the tour takes less than an hour. It looks like you would have plenty of time to see the grounds, visit the gift shop, and/or have lunch before catching the bus to Hatzenport.

So, yes, it looks like Burg Eltz and the Marksburg in a day would be doable. Combining a cruise from Rüdesheim with a Marksburg tour would also be possible, but you probably want to get off the boat in St. Goarshausen. It's a short walk (about 4 or 5 minutes) in St. Goarshausen to the station from which you take the train (21 minutes) down the right bank of the Rhein to Braubach. You might want to board that cruise in Bingen rather than Rüdesheim so you don't have to cross the river in the morning. BTW, you go to Bingen Stadtbahnhof, not Bingen Hbf to catch to boat cruise.

It will probably work getting there at 9:30. We got to Burg Eltz closer to noon and it was around 4 by the time we got back to Hazenport. We had originally planned to take the train to Cochem for an early dinner, but Burg Eltz took more time than we anticipated.

When we got to the Burg Eltz parking lot it was just starting to rain, so we did take the shuttle to the castle. Once inside the courtyard we had quite a long wait due in part to the limited number of English tours and a person getting ill somewhere along the way that needed to be helped out. After the tour the shuttle line was long, so we chose to walk back to the parking lot. Along the way we did stop to find the oldest active geocache in Germany which probably didn't delay us because we got to the bus stop just before the bus did. Even if you take the shuttle both ways, take the time to walk the path next to the castle stop for good viewing of Burg Eltz.

We did the round-trip Boppard/Bingen cruise. It was a beautiful day to be on the river, and we were happy with the cruise we chose.

The Bahn website claims there is also a bus from the station to a
cemetery, from which it is an 11 minute walk to the castle.

At the DB site: Enter "Burg Eltz, Wierschem" as your "from" station and "Braubach, Marksburg" as your final destination. You will see a 12:22 departure with arrival at Johannisfriedhof (cemetery) at 14:18... plus... instructions to walk one km (estimated at 13 minutes) from there to Marksburg (final arrival, 14:31.) The bus/train connections are provided as well.

The same journey is possible at 13:22 as well, with final arrival 15:31.

The bus to Johannisfriedhof won't get you to the castle earlier than walking; you will step off the train in Braubach at :05 after the hour, so a walk of 25 minutes (which is what I spent getting up the hill) will get you there at :30 after instead of :31 after.

We are thinking of taking a river cruise from Rudesheim to St Goar
another day, so maybe Marksburg fits better that day.

Your day begins in Boppard, correct? So you'd need to leave Boppard early to get there. Ferry across and walk into Filsen for the 9:13 train to R'heim (9:52), then a cruise from R'heim (11:00) to St Goarshausen (12:50) could be followed by a direct train ride (13:02 or 13:32) to Braubach (13:33 or 14:18 at Johannisfriedhof, or earlier at Braubach station.) You would have time for lunch in Braubach, but only an hour in Rüdesheim. So this would work if your goals in R'heim are modest.

Thank you, all, for your assistance. I like the idea of seeing a castle, taking a break on the train, then seeing another site in the afternoon. I will add that I spend quite a bit of time on the DB site planning routes, but I don't always know the specific station I'm trying to get to, or which option provided by DB I should be choosing, making me question some of my results. I appreciate the specificity provided above. Thank you.

I would suggest doing both on separate days, using the trip to Burg Eltz as a reason to explore the Mosel, particularly Cochem.

When we hit Marksburg last summer, it was on the drive to Rudesheim. In the summer, there's a 1:00 English tour. Maybe save the Rudesheim to St Goar cruise (which we also did) for another day. You chose well in Boppard as a jumping point.

Another vote for doing it on several days although a single daytrip might be possible when you in a hurry

The tour at each castle lasts about an hour and neither castle is near the train station. When we visited Marksburg the English tour was 1pm. There were no self-guided tours at either castle. We visited the castles on separate trips and had a rental car.