Athens - Santorini - Mykonos

There doesn't appear to be any ferry scheduled after October 11 that will take you from Santorini to Mykonos. There is a ferry from Paros to Mykonos at 11:00-11:40am, but there is no ferry from Santorini to Paros that will get you there in time to catch it on the same day. But if you reverse your itinerary and go to Mykonos first you'll be able to catch the 10:00-10:40am morning ferry from Mykonos to Paros and then take the Blue Star ferry at noon the rest of the way to Santorini.

Also, today I received an email newsletter notice from Aegean Airlines that they've just released some 'saver' fares for their domestic flights starting in October, €39 from Athens to the islands and €29 from the islands back to Athens, all taxes included. I suggest you check out their website to see what's available on your travel dates.

http://en.aegeanair.com/Default.aspx

Brotherleelove is correct. Santorini and Mykonos are on two different ferry routes, connected in summer by small catamarans - the last direct catamaran service ends on Oct 11th. The ferry from Mykonos to Paros is your only possibility for getting between Santorini and Mykonos without going back through Athens. That ferry, SeaJet 2, is another small catamaran operated by a company with a less than sterling record this summer.

You would simplify matters by going to Santorini first, as planned, then stopping at Naxos or Paros for your second island. They are on the same ferry route as Santorini, with several daily ferries back to Athens. Were it me, I would choose Naxos for it's mix of beautiful chora (main town) and interesting inland villages.

Hope you post a trip reporyt! We are looking at doin the exact same trip next September - any advice would be appreciated

As I have read, you will have some free time when you are in Athens. I have been there several times in the past and I would suggest you to take a look to the Greek capital too. You should not omit visiting the Acropolis Museum and of course Acropolis. Taste the famous kebab at Monastiraki (you can go there easily by metro) and walk around the town. It is usually sunny during October, so you will love that blue sky. Before my first visit in Athens, I found a map (it included a city map and a map with the metro and the train routes) that helped me about how to move there and which places to visit which was really useful to me. I post the link in case you are interested in it:
http://www.athens-greece.us/athens-maps-greece.asp