I agree that a cruise will lull drowsy travelers into sleep, and you don’t wanna miss it by sleeping through it. Save it for when you’re feeling most awake. Bacharach is quiet and cute, which makes staying awake a challenge. But it will be easier to explore in your jet lagged state than a bigger city. You’ll have a couple days to take it easy, so you’ll be nice and relaxed to kick off your vacation.
As for itinerary suggestions, I went to Germany the last two weeks of July 2019. I spent my last two nights in Bacharach, so didn’t have jet lag considerations anymore, but I was ready for the more relaxing pace of Bacharach. My vacation had been getting hotter and hotter. I was just under 90F in Munich in a hotel with no AC. It was even hotter in Bacharach. I arrived around 4pm, got settled in my room and took the earliest seating at Stuebers restaurant (no AC), then napped until about 30 minutes before sunset (I actually looked up the time of sunset). That gave me time to wander around Bacharach as weather was cooling. The next day I wanted to hike to Burg Eltz, as described in the RS guidebook. I was worried because it was so hot, so I woke up earlier than comfortable to arrive at Burg Eltz as soon as it opened. Train to Koblenz, change to train to Moselkern, hike. The hike was my favorite part of the Bacharach portion of my trip. I loved the castle too. After the castle, I had lunch in Koblenz (I had a pretty long wait before next train to St Goar). In St Goar I climbed up the hill to Burg Rheinfels. It was oppressively hot, but I had water and survived. My visit to Rheinfels was short, but I think your young boys will like it. Then I took a boat cruise back to Bacharach, dinner, and sleep before heading to Frankfurt airport the next morning!
With your schedule, I would assess how tired I am when I arrive in Bacharach. How much sleep did I get on the plane? How long did the train ride take? Is my room ready? I might have the energy to take the train to St Goar and see Burg Rheinfels. But I might be too sleepy, so I’ll wander around town until room is ready, then I can nap until dinner. Once fed, I might be awake enough for the last river cruise (downstream to St Goar, then train back), but I might feel better leaving that ‘til tomorrow. Next day I’ve got an alarm set to force myself awake early. There’s some time for a few zzz’s on the train, then the walk to Burg Eltz will let me breathe the fresh air of morning, so I’ll be awake enough to enjoy that tour, and I’ll have an entire day to explore the rest of the Rheinland. I can take the river cruise upstream back to Bacharach. I can wander around Bacharach, or I can sleep some more, so I have more energy for the rest of my vacation, wherever that may take me.
Have a great trip!