I'm guessing your train will go through Köln/Cologne; my standard response is to always store your luggage at the Bahnhof, and take at least 2 hours to visit the Cathedral next door. Take more time and have lunch...and some Kölsch...at one of the nearby restaurants ;-) You'll have to skip the lunch...and probably the Cathedral (!) to make the 14:00 boat, though. You can always have the Kölsch ON the boat ;-)
Assuming your trip is between April and October, yes, you can do this. I've traveled from Koblenz to St Goar (plus many other routes over the years) but that takes awhile; your trip will last 2 hours. You can get a 20% doscount with your SelectPass (or German rail ticket), and any seniors can get up to a 30% discount. This will not use up a day of your pass. Yes, you'll need to buy tickets at each boat dock before your departure. (You can HOHO with a GlobalPass, however.) I always suggest the Goethe boat at 9:00 when possible (you can have a great breakfast onboard!), but this will be pretty early for someone coming from Amsterdam :-( Your next choices are 14:00 or 18:10 (this one is on a different company's ship, but they look the same as the K-D boats to me...). In Koblenz, the boat dock isn't terribly far from the train station, but it's not super close, either. Plan accordingly. The trains will arrive in Koblenz around 13:45, so it'll be tight getting to the dock and getting your tickets purchased. An earlier train arrives around 11:45, giving you some time to check out Deutsches Eck, grab a quick lunch, and/or stroll and hang out near the dock.
To extend your time on the Rhine, you can also just buy train tickets that travel along the river. You can buy them from the machines at the stations, and there are many more departure times for the trains than for the boats. This way, you can visit a few of the other towns along the bank. Maybe even take a boat back to Boppard, if you'd like.