Is there a way to get from Istanbul to Athens by train or ferry.
It is a very long trip and you would need to change types of transport. On the other hand, it's a little over 4 hours to fly and that is a lot less hassle! www.rome2rio.com/s/Athens/Istanbul This link will show you the options.
We flew on Turkish Airlines. Although that 14 hour bus route looks interesting, it's all in Greek. And it appears that you might have to change buses.
I would fly. Buses/ferries will take up a day or most of a day and a night. If you do opt for the bus, there are plenty of places to break up the trip (I took a 19-hour bus ride once in Turkey, it was excruciating even though the hospitality on board was great).
we are traveling between Istanbul and Athens soon and the flight time is one hour and 30 minutes.
Aegean Airlines/Turkish Airlines have regular flights and the fare is inexpensive/reasonable if you buy
your ticket early.
Flying is the only practical way. There is no train. Ferries usually require a long (overnight) ride to a "border" island such as Lesbos, Samos, Kos, or Rhodes, then a local connection to the Turkish coast, for which you may have to wait an additional day, but that's still not getting you to Istanbul.