I have always found this website the MOST comprehensive & reliable http://www.gtp.gr/RoutesForm.asp -- it isn't limited to ONE company -- it also shows the routes on a map. If you want to get the complete picture of the pattern of service, you put in your departure & destination ports, click on the Month you want, and for day, leave at "Any" -- then you will see ALL available sailings.
Adam, you are going in Off-season, so booking more than a few days in advance is not really necessary ... except for 2 key dates. (BTW when you ask advice on these forums, it's thoughtful to say clearly the exact dates you arrive AND leave Greece; it's helpful). The weekend of June 3-4-5 is "holy Spirit (Pentecost) weekend" ... w Monday holiday == and it's traditionally the first Summer weekend of year when people POUR out of Athens to the Islands -- espc. the college students who've just finished their cruel final exams! Thus, ferries outbound on Friday June 2 will be heavily booked, and also ferries inbound to Athens on Monday JUne 5 & Tuesday AM.
It would be wise to book upon arrival for either of those dates, if you are taking a so-called "fast-ferry" out of Athens or Rafina -- those vessels only hold 400-500 max. The BIG "conventional" ferries like Blue Star hold from 1300-1800 passengers so, not to worry, however if sailing a big ferry on those dates, for a journey of 4 hours or more (ie Paros/Naxos), it would be wise to book "reserved economy" an inside, numbered seat (ask for a Side-section seating, near window) instead of just "economy, which only entitles you to deck seating, or a chair in a cafe or in corridors, first come/first served. This doesn't mean that "reserved" passengers are stuck indoors. You can sit on deck wherever you can find a chair (the plastic patio-variety), and only come indoors when you want to rest or snooze.
If you arrive May 28, and want to book for June 2 - 5, the easiest way is just to go to one of the 2 travel agencies in the airport -- Amphitrion or Pacific Travel -- and buy the ticket(s) on the spot. NOTE: if you would try to book "reserved economy" online for Blue Star, you're not allowed to request seating location... just another reason not to do online. The agencies charge an insignificant convenience fee... €1-2 per transaction.
