I did a similar trip a couple of years ago and if I had it to do over again I would take the ferry from Athens to Mykonos right away on day of arrival and visit Athens on the back end - that way you can nap and relax on the longest ferry leg when you are tired from jet lag and there is nothing to do but watch the water anyway. There is good high-speed ferry service for going on from Mykonos-Santorini. Then you could fly from Santorini-Athens, spend your 2-3 days in Athens and fly on to Istanbul.