Flights:
ATH dp 08.30, fares start at 86 EUR (skyexpress)
ATH dp 10.00, fares start at 114 EUR (skyexpress)
ATH dp 10.10, fares start at 144 EUR (Olympic)

Fast ferry (only if your plane arrives in time):
Rafina (to reach by taxi from Athens airport) dp 7.15 - Santorini ar 11.30, Fare 45 EUR
If the fast ferry is fully booked, you may take the slow ferry
Rafina dp 7.55 - Santorini ar 16.30, Fare 35 EUR
Tickets at Rafina

Good point by neckervd on the ferries from Rafina, which will still be running to Santorini at the end of September. The slow ferry won't be fully booked, and IMO is a better choice than the highspeed.

The Olympic fare shown by neckervd for 10:10 on the 30th is GoLight, which is carry-on only (actually €149 this morning). If you have checked bags you will pay extra, bringing the total up to nearly the Flex fare. If you wait and pay for the bags when you arrive at the airport you will pay more than online, and won't be able to use the baggage drop-off point. MORAL: book Flex, which includes 23kg checked baggage & 8 kg carry-on, and has better terms for changes and cancellations.

I haven't checked the Sky Express fares, but they have several different weight limits for checked baggage and carry-on, so look carefully when booking. I believe Sky Express uses the ATR-42 turboprop, while most Olympic flights are with the larger Dash 8-Q400.

I use the Aegean Airlines website, which has all the flights for both Olympic and Aegean, since they are part of the same company. Flights with the Aegean logo are usually with Airbus A320 series jets.

I flew with Sky Express to Santorini last August. Our flight back to Athens (from Milos) was with Olympic. The prices were much the same but we vowed never again to fly SkyExpress. Why?

They had no system for check-in - everyone joined the same skyexpress queue even if you were going to Paros, Naxos, Santorini etc. The queue barely moved, so as it got closer to departure times they would just shout out "Paros" and everyone going to Paros would go out into a separate queue where they were dealt with in preference to everyone else. Which then meant everybody else just stayed in the queue while the Paros people were processed. They did have a separate queue for people with electronic / pre-printed boarding cards, but you had to organise that more than 2 hours before the flight, and we hadn't, so we were stuck in the same queue. On our way back through the airport 2 weeks later we passed by the Sky express queue and the same pandemonium reigned.

Our flight was delayed, so we called the rooms where we were staying in Santorini as a transfer was included, so we wanted to let them know we were delayed. Their response was "don't worry we always check before going to the airport; Sky Express is always late anyway". Olympic left and arrived bang on time.

The baggage allowance with Sky Express is TINY (6Kg in carry on and not much more in the hold on a standard ticket). There are lots of different ticket types, and the bags are MUCH cheaper if you buy them with the ticket or before leaving, the excess charges are really steep. Olympic by contrast gives you a decent carry on and 23kg in the hold as part of a standard ticket.

BUT for you, I wonder would Sky Express be a better choice than a more organised, reliable company? I say that because if if your flight is delayed from the US and you are joining a long check in queue with minutes to go until your flight closes, you will be pulled out of it. Because SkyExpress check people in so close to departure time they also give you (as a late check in person) a fast pass which means you get to go through an express security gate. Plus there might be more chance of a corresponding delay with your Sky Express flight.

On our trip to Greece a couple of years ago, we flew from NY to Athens and then immediately to Santorini. There was a flight leaving about an hour or hour and a half after our flight arrived, but did not want to risk that so took one a couple of hours later. As it turned out, we were on time or early into Athens, got through immigration and got our bags very quickly, and could have made the earlier flight. But would have been very nervous the whole time. So we had a couple of hours to wait in the airport, not the end of the world, and for us, safe was better than sorry. But the process was very easy. Got our bags, took escalator right upstairs and checked in for our flight to Santorini and dropped bags off. Entire process was quick and easy. But again, we were just too nervous about cutting it too close so played it safe. Would not want to have started our vacation missing our flight and scrambling to buy another ticket to Santorini.

We are arriving from US to Athens at 1:30pm and our flight to Santorini is at 5:15pm.
Should we keep it at 5:15pm or take the mnext one at 7:40pm?
They are both with Aegean/Olympics.

Please advise and thanks,.

Keep the 5.15pm flight, even that is too much time.

This is a three year old thread, but to answer your question 3hrs 45min is more than enough time for a connection. Since both flights are with Aegean/Olympic you can check in online for both flights before you leave home, and print or download your boarding passes. There will be a bag drop off at Athens Airport, and Aegean Connection Ambassadors there to help.

Thanks so much, everyone here.
*
By the way, any recommendations for a driver to do Delphi and Meteora with overnight in Meteora (1 night) and then back to Athens?

Much appreciated.
Thanks,