Listed as a UNESCO World Heritage site, there are several options to explore Rhine valley from Frankfurt. The most scenic stretch is rated to be between Bingen(or Rudeshiem on the other side of the river) and Koblenz. Beyond Bingen, towards south, there is the city of Mainz while beyond Koblenz, to the North, there is the city of Cologne. A cruise is a must to enjoy what the Rhine Valley has to offer and you need to decide how much time you want to spend in the boat – half a day, full day, 2 days? Also whether you want a return trip or just one way? You will also have the option of hopping on and off the boats.
If you had only 1 day
If you only a day to spare, best to take the train to Rudesheim, spend some time there, take the morning or afternoon cruise-either 1.5 hours return cruise or a longer 4 hour return cruise that goes upto Loreley Rock(St. Gaur), and board a train back to Frankfurt late in the evening. I personally think the 4 hour cruise is good enough to see the best of Rhine Gorge.
Another option, is to take the cable up to Niederwalddenkmal, walk through the forest and then take a chairlift down to the town of Assmannshausen, and from there, a boat to Rudesheim. It is only a short 35 minutes or so journey by boat but long enough to see 3-4 castles on the hill side, some of them in ruins and some converted to hotels and get a sense of how the longer cruise would be like. More like a trailor.
Tickets for cable car, chair life and boat can be purchased in Rudesheim and costs ~25 € per person. A return boat ride to St. Gaur also costs about the same.
View of Rudesheim, Rhine river and vineyards from cable car Chairlift down to Assmannshausen, Germany
Train journey from Frankfurt is very scenic
The train journey from Frankfurt is quite picturesque once the train reaches the Rhine river, with the mightly river on one side and vineyards on the other. And the train passes through some beautiful villages.
Rudesheim is a beautiful town and very touristy. Other than Niederwalddenkmal, a historic monument on the hill top offering spectacular views of the river and the valley, there are couple of castles if you are interested. You can also stroll around the town, and on Drosselgasse, a narrow lane with plenty of wine taverns and live music or if you like to be left in peace, sit in a café/bar overseeing the river. Rudesheim is actually a wine making town and hence a good place to taste local wines.
Main street in Rudesheim, Germany Drosselgasse, famous lane in Rüdesheim, Germany
Synchronise train and boat timings carefully
Do ensure the train and boat timings are synchronized well with reasonable gap. There is a tourist Information office in Rudesheim where tickets for cruise, cable car, and chair lift can be bought. Train tickets can be bought at the station. Tickets are not available on board.