Until June, 2007, Delta and Olympic are the only 2 airlines that fly directly to Athens from the States. Continental starts non-stop service to Athens, from Newark, in June, departing at 5:30 p.m. and arriving at 10:20 a.m., a terrific time to arrive. From NY, Air France via Paris is a great flight because it leaves JFK at 5pm and gets you into Paris with enough time to catch an early bird flight to Athens and you are able to make one of the late morning flights over to the islands. Take your pick.  

Aegean Airlines and Olympic are the only 2 airlines that operate flights from Athens to the islands. There are some other charters, but they are normally the same price as the others. You can also opt to do Mykonos first and then hydrofoil over to Santorini and get back to Athens from there.  

Hydrofoils will run regularly so long as it is not terribly windy. Once the Meltemi winds kick in, they may cancel the hydrofoils. Unpredictable, and sometimes they cancel at the last minute. But you can usually figure it out a day in advance and plan to fly to Athens and then to Santorini if you had to. Many people recommend not purchasing the hydrofoil tickets until you get on Mykonos. They run from Mykonos once a day at 2:30 and will get you into Santorini by around 5:30 (stopping at a couple of other islands in between). The port is in town and about an 8-10 minute ride via taxi. There is NO need to get there an hour before, they never leave on time anyway. This is Greece! And if you HAD to fly, flight availability at the last minute should be no problem in September. The hydrofoil mode of transport to Santorini is highly recommended. The view on the approach to the island from the water is something that cannot be described.