Very valid question and one that unfortunately I'm not going to be able to answer until closer to the game.
As it stands, it looks like all forms of rail transport from Piraeus to Athens stop by around half midnight during the week. I arrive the week before the game so we will immediately ask the staff at the main stations. The hope is that common sense will prevail and an extended Metro service will be put on through the early hours, I know this has been common in the past for concerts etc.
Everything is left until tomorrow in Greece so I don't think I'm going to be able to get an answer on this until very close to matchday. The other option to cover yourself is perhaps look at digs in Piraeus so at least you can get back home within around a 30 minute walk. I know that goes against a lot of advice I've given regarding possible central locations for accomodation. I will of course try to find out more on this but hopefully not another Istanbul on our hands.
@Alex - City Matters, apologies to namedrop you directly, but is this something you or a colleague could perhaps look into through the official channels, on our behalf? Presuming City and UEFA will be in dialogue over such matters. Thank you.