it was way cheaper to fly into istanbul
stayed at the side hostel (see-dah), right next door to the four seasons istanbul. they also have a hotel. very clean rooms for very cheap, with a good breakfast on their wonderful patio upstairs (with great views of the blue mosque and the hagia sofia).
when going from istanbul to athens, take the plane. train takes for damn ever because there is no high speed service in turkey.
you could also island hop via ferry, but it'll take a while as well.
athens can basically be done in 1 or 2 days.