Whether Mykonos or Athens is 'best' depends not only on the sync calculations but also on whether you want to travel through the Athens/Piraeus area or stay a night on Mykonos.
The ferries from either point do conform to a pattern of departure times there is no problem about that.
I prefer to use Mykonos as I've done the via Athens/Piraeus bit so many times to get 07:30 ferries to the Cyclades it became tedious.
The last time I went from Mykonos at a similar flight arrival time, it was 14:15 departure or wait until a possible evening departure of maybe around 20:00.
To simplify that 1 night on Mykonos settles any will you/won't you make the 14:15 ferry, or a long wait.
Coming back you will have to overnight on Mykonos just due to ferry timings from Syros.
People might say that's expensive but you do save on the longer ferry cost from Piraeus. Relaxing on Mykonos is better than crashing thru Athens/Piraeus on the X96 bus at 04:00 dead tired.
Book your nights on Mykonos, it's tedious looking on arrival on Mykonos in paricular by that time of year.
Edited: 21 May 2013, 11:54