Having done similar things, I'd say the plans are about equal, though the second one means getting up very early (if I understand it.)

The Sofitel is excellent and about a 60-second walk from the terminal. It's expensive, but there are often cheaper rates on the web sites, usually with a more restrictive cancellation policy than the rack rates. Their restaurants are quite expensive, but you can get simple meals at the airport food station.

Do the plans involve seeing Athens on different days? If so, you should check site and museum hours. I my past experience, the biggest sites and museums are open daily, while less important museums are closed Mondays (public Museums) or Tuesdays (private museums). Many sites and museums have reduced hours on Sundays. Also check to see if you'll run into one of the "floating" religious holidays, when some things might be closed.

As for the ferry, if you want to splurge it might be better to get a first class ticket rather than a cabin, unless you actually want to sleep. First class costs in my experience 20-50% more than economy. Usually it's not worth it, but for a seven hour trip where you want more comfort you might find it justifiable. The main advantage is that first class (often called VIP class) can be much less crowded and quieter; it also has more spacious and comfortable seats, usually a significantly nicer outside deck area, and sometimes a better (though more expensive) restaurant or cafeteria.