Help navigating both sides of Rhine

Last question first. Probably closest station to access the K-D boat from the train station is Bingen (Rhein) Stadtbahnof. Its about 1/4 mile to the K-D dock. You can get there in 1 hour from the airport regional bahnhof, but you will have to change trains at Mainz or Bingen Hauptbahnhof depending on the routing and time you get to the station. trains about every half hour.
Second question. R-P ticket is not good to Cologne. The "state" border is just south of Bonn. But you can use a Quer durch Lands ticket or Schoenes Wochende Ticket.

Köln, and Königswinter are in Nordrhein-Westfalen, not Rheinland-Pfaltz, so I don't think the Länder ticket would work. Linz, however, is in Rheinland-Pfaltz.

Never visited Drachenburg, so can't help you there.

The easiest place to catch a Rhine ferry from Frankfurt Flughafen is probably Rüdesheim (Bingen is on the opposite bank of the river from the airport).. Not positive, but I believe you can take a commuter train directly there without any changes. I don't know precisely how long this would take, but it seems like a perfectly reasonable plan for day one. Everything is easy to find, I don't see how you could get lost.

"I'd like to go up to Koln & back just for a quick look around near the cathedral. I'd like to stop in Linz & Konigswinter along the way.
1. How/where should I cross back & forth"

The train out of Koblenz crosses the river for you on the way north to those cities and Cologne. No ferry needed for the return trip either.

An R-P ticket gets you to Bonn (even though it's north of the R-P border) but no further. You can add on the Bonn-Cologne VRS fare (less than €8 as I recall each way if you're on local/regional trains.)

The train/boat timing is better if you board the cruise in Bingen (you'll likely be waiting an hour or so for the boat to leave in Rüdesheim.) You can get a direct train from Frankfurt Hbf (main station) to Rüdesheim, but not from the FRA airport station. So you'll need to change trains once whether you go to Bingen or Rüdesheim.

First question. Train from Boppard to Cologne in the morning on Regional train. Returning take the regional train that crosses the Rhine at Cologne and goes along the east bank of the Rhine, stopping at Koenigswinter and then Linz and final crossing the to the west bank at Koblenz. Koblenz back to Boppard on regional train.
The regional trains from Cologne to Koblenz on the east back go every half hour and stop at both K-W and Linz. With a QdL or S-W ticket you can hop on and off. There may be other slightly cheaper ways with intimate knowledge of the VRM and R-S transport unions.

OK, after researching the VRM and VRS websites, I've come up with this.
Traveling after 9 am weekdays or anytime weekends, you can buy a VRM all zone tageskarte for 18.50 euro.
That covers you from Boppard to the VRS Border at Bonn Mehlem, and from Bad Honnef on the VRS east bank border back to Boppard. Unlimited travel on buses and regional trains.
Next you would need a VRS price level 3 tageskarte for 13 euro. That covers you from Bonn Mehlem to Cologne then to Koenigswinter and then to Bad Honnef. Unlimited travel on buses, trams, U-bahns, and regional trains in the zones between Bonn, Cologne, Koenigswinter, and Bad Honnef.
That brings it to 31.50 euro total. A bit less than a QdL ticket of 44 euro or a Schoenes Wochende Ticket for 42 euro. What I don't know is how to get the VRS ticket without getting off the train in Bonn and buying it out of a vending machine then waiting for the next train.
Another thing, if you are planning on staying in Boppard for a few more days, you can get a 3 day VRM tageskarte for 37 euro. Then you can travel the whole region for 2 other days. Down to Oberwesel on both sides of the Rhine, and up the Mosel past Cochem to Bullay.
Here is the VRS transit map: http://www.vrminfo.de/fileadmin/data/pdf/2015/Liniennetzplan_2015.pdf

"Traveling after 9 am weekdays or anytime weekends, you can buy a VRM all zone tageskarte for 18.50 euro."

Actually, the ONE-person version of this type of day pass has no before-9:00 travel taboo; same for the 3-day version. The 9 am (weekdays) rule applies only to the mini-group version (they don't want groups of 4-5 clogging trains during morning commute hours.)

VRM ticket info

I'm fairly certain that if you made a stop in either Remagen or Linz am Rhein, both worthwhile stops, you'd be able to pick up the VRS tickets you need.
Or maybe you can buy online at the VRS site (I haven't tried buying on the VRS site myself.)

Thanks Russ, assumed it would be the same as a Laender ticket and I've only ever used the mini-group ticket.
Regarding boat pick up spot, looks like Ruedesheim also requires a change at Mainz/Kastel, connections are only once an hour, takes an hour and 45 minutes, and the walk to the K-D dock is 15 minutes. So Bingen Stadt wins in all 4 categories.

"Ruedesheim ...takes an hour and 45 minutes..."

I think that time is for a trip from FRANKFURT HBF. The OP is coming from FRA airport, as I understood it, so 1:20.

From the airport, take the train to Wiesbaden and switch there to the dedicated train that goes up and down the right side of the Rhine every hour. If you get off in Assmanshausen, you have more time to catch the ship as it goes to Bingen after it docks in Rüdesheim and then goes to Assmanshauen. The dock there is fairly close to the train stop. I have done this a number of occasions and it works really well. Otherwise, it is nice to walk around Rüdesheim for 45 min. or so til the next ship comes.

Thank you very much, everyone!

I think I now have a few options, depending on plane arrival:
1. 9:59a train to Bingen arv. 10:59a via Mainz & 11:30 ferry arv Boppard @ 1:50p
2. 10:44a train to Assmannshause arv 12:09p via Mainz-Kastel & 2:45 ferry arv Boppard @ 4:50p
3. I think I found a direct train dept 11:24a arv Boppard @ 12:39

Questions re: VRM tickets...
4. Am I correct in thinking that these are different trains ( not DB) but that they run on the same tracks? so if I get a 3 day VRM for River area (minus Trier & Koln) I would need to look for trains marked VRM but can jump on any of those at any station? Are there separate ticket machines or are all lines on same terminal @ stations?
5. Do I need to get any tickets (VRM, DB) validated prior to boarding? In Italy there were punch machines on the tracks so wondering if Germany works the same way. Is there anything special/ different for passes vs single tickets?

Thanks again,
Carrie

?4. The local trains on the west bank of the Rhine are operated by MRB, Mittel Rheinbahn. There also DB Regional Bahn and Regional Express trains and you can also ride these. You can't ride IC, ICE, or EC trains as these are long distance trains. So it not the name on the train but the class of train that is important.
?5. I believe you do have to validate the first time you use it, but I can't remember as it was a VRM Minigroup ticket and if it was done, it was just the first ride. After that just keep in your wallet and show it if a conductor asks. Doesn't happen very often.

No validation needed. Only certain cities in Germany have validation requirements and the machines to do so. Frankfurt, Mainz, the Rhine area, etc. do not have this. The tickets are either time stamped or they are all day tickets. With time stamped tickets you have a certain amount of time to get to your destination. So, you wouldn't buy a one way ticket in the morning and then hope to use it that afternoon.

2. 10:44a train to Assmannshause arv 12:09p via Mainz-Kastel & 2:45 ferry arv Boppard @ 4:50p

The train to Assmannshausen will zip past the Niederwalddenkmal, Ehrenfels castle, and the Mäuseturm, all nice sights to see from a boat deck. I'd advise starting from Bingen (or Rüdesheim) instead.

TRAINS: You can hop on any trains but the high-speed trains - no IC, ICE, EC trains. Check the train SCHEDULES for these designations. MRB, Via, RE, RB, etc. are fine. There are only a handful of high-speed trains that stop in Boppard. In Koblenz, there will be many. Electronic boards in the main Koblenz station will show the designations clearly. Posted departure schedules like the ones in THIS PHOTO (yellow; white are arrival schedules) are in all stations on platforms and/or walls. HERE is a close up that shows the train designations.

THIS is a photo of the Boppard trackside ticket machines. You should be able to get the VRM ticket from both - the machine should have a VRM logo.

You understand that the VRM ticket is not valid between FRA and Bingen or Assmannshausen, right? The RMV ticket machines at FRA will sell you tickets for that stretch. Show your RMV train ticket at the KD dock for a 20% cruise fare discount.

You guys are awesome! And as a visual person- thanks for the pics, a big help. The train schedule board reminded me that I need to look up train final destinations, something I learned in Italy but forgot about.