If you just want to go to Germany and Greece, definitely fly between the two countries. With low cost carriers, it'll be as cheap or cheaper than 35 hours on a train, and take about two hours. Keep your options open about where you fly in and out of, too - you don't have to fly to Athens - low cost carriers go to Thessaloniki as well, and you could fly in there and out of Athens, covering more territory in Greece.
Heads up, though, a lot of the smaller hotels and pensions shut down after the season, and some of the ferry connections are reduced as well, so read a good guide to Greece and do lots of research on line to make sure you can actually get to the places you want to go, and have a place to stay there.
But be flexible - you might find another place that is open and accessible and will have a great time there, too. We had a hard time finding a place to stay in March, but the one we did find turned out to be a great option and in a place we'd never considered.