OR is there somehwere else I am missing in Germany? ( We are ending our trip in Berlin)
It's a tough call, I think. Early April can be cold. I've run into snow then myself. And while "things" are open, most of those Rhine things involve time outdoors... those cruises can be numbingly cold. The chairlift rides, the town-wall walks, hiking/biking, Rheinfels Castle (a largely outdoor experience since it's a set of ruins... these and others will be impacted if the weather isn't right. And there's really not much indoor excitement in Boppard. So I think a better Rhine strategy might be to play it by ear... and yes, there's much you will not see in Germany, and some good stuff nearby... Try this...
Day 1: Travel to Mainz for a 3-night stay. But travel on a flexible ticket (day pass for example) and make a stopover somewhere on the way that interests you. Take a cruise or do the hike to Marksburg if the weather is inviting, and if not, pick something indoors instead, either in Mainz (which has several good museums and similar) or elsewhere.
Days 2&3: Good weather? You're about 30 train minutes from Bingen for your Rhine cruise, a little further from St. Goar, Bacharach, Oberwesel, and Boppard, all of which are served by train. Rüdesheim across the river from Bingen isn't far either. Not so good? Mainz may have more for you. Or take the train south to SPEYER, which is surprisingly full of interesting things to see/do. Day passes like the Rheinland-Pfalz ticket make these outings simple and cheap.
From Mainz you'll be just 25 minutes from the FRA terminal by direct train.