Rail pass or buy tickets ahead of time

Best value is really subjective. Price of p2p tickets depends heavily on dates/times of travel and how far in advance you purchase. You can price out individual tickets on your own using the db itinerary search page. My first hunch is that the German Rail pass will be a more convenient way of getting around and worth a little extra (if indeed it costs more.) No advance purchase is required (you can buy it in Germany if you like) and it involves only ONE purchase (vs. several individual tickets.) It can also allow you to adjust your itinerary here and there without making ticketing changes.

Bonn - (Rhine cruise) -Mainz

Any cruise you do with KD gets a cruise discount of 20% as long as you have a valid train ticket or pass for reaching the KD location - ANY ticket will do - so rail passes offer no special cruise discount advantage.

The cruise between Bingen and St. Goar (or Boppard) is the best part. Cruise just that 1.5 - 2.5 hour stretch, and you will save both time and money. Use the train for the rest of this Bonn-Mainz gap.

Also, the cruise is only a small part of the Rhine experience. The area between Boppard and Bingen - the Upper Middle Rhine Valley - is ripe for a couple days worth of exploration (castles, wineries, old-world towns, great scenery.) Consider making time for it.

http://whc.unesco.org/en/list/1066

https://www.tripadvisor.com/Attraction_Review-g642094-d268085-Reviews-Marksburg_Castle-Braubach_Rhineland_Palatinate.html

https://www.tripadvisor.com/Attraction_Review-g198627-d3306006-Reviews-Sesselbahn_in_Boppard-Boppard_Rhineland_Palatinate.html

https://www.romantischer-rhein.de/uploads/pics/Altstadt_02.jpg

https://upload.wikimedia.org/wikipedia/commons/4/4c/Bacharach_BW_9.JPG

We don't buy extra days on the pass for in-city transport, since it's the cheapest distance. S-Bahn is covered on the counted travel days of the German Rail Pass (and could be useful on your way to/from a longer train ride), but not U-Bahn, tram, or bus. Ferry discounts don't require counting a travel day. You might use a pass for 5 or 7 travel days within a month, with travel-together discount, $190 or $237 per person, respectively. Of course, if you spring for a consecutive-day style of pass, then you're not counting days in the same way.