We have stayed at the Sofitel and it is definitely handy but it is also so sterile. It could be a business hotel in any city in the world.
I prefer my last night in Greece to FEEL like Greece, so we have over the years stayed in several b&b's near the airport. Last fall we tried the Avra Hotel, recommended by many people on this board, and it was wonderful. The hotel itself was very nice, with an elevator and comfortable rooms -- some with sea-view balconies. It's just a short walk to the port at Rafina, where you can choose from a variety of tavernas for your farewell dinner, and watch the ferries returning to port, ready for the next day's journey. The Avra has a free shuttle to & from the airport -- you'll need to arrange that when making a reservation. They know what time to get you there for your flight.
Edited to add: I just realized that you may be spending your last couple of nights in Athens. In that case, you may not want to change hotels, so a 3:30 am taxi would get you to the airport in time. But if you have the option to stay near the airport, I would pick the Avra. In fact, we've reserved it for our trip this coming September.