The two primary means of travel in and among the Greek islands are by ferry boat and by plane. Each has its pros and cons. Flights are the quickest and are more "guaranteed" than ferry boats. Most flights to any given island are an hour max, some as short as 20 minutes. Check-in an hour prior is required at the airport, however. Baggage claim is faster than the in the US, which is good because the overhead compartments are smaller than on US planes. Further, very few flights go between the islands. Most require flying back through Athens, which can add a lot of time with plane switching etc. (Athens airport is clean, on the smaller side and easy to get around though.) Flights are also more expensive. They do, however, run sales and can be low as 19 euros one way (plus taxes). The two primary airlines are Aegean Air and Olympic Airlines (more routes). We flew both and each was clean and efficient.
Ferries are a more popular means of travel in the islands, some of which may be hi-speed catamarans or hydrofoils which are 2x price and speed. They are cheaper than flights and every island has some sort of ferry service, on rare occasions they can be cancelled due to poor weather conditions (mostly the smaller local ferries). For this reason, it is generally recommended to give yourself 24 hours buffer between the ferry and your homebound flight out of Athens. The schedules can also change at the last minute. It is useful to have a flexible schedule and to check on schedules and buy tickets near to the day of travel.
The ferries are not particularly clean on deck seats and there are not assigned seats, it's a free for all scenario. Luggage is best kept in close proximity to your seat . Both the Blue Star Ferry and the Seajet catamaran have A/C, bathrooms and lounges for snacks and drinks. The Blue Star Ferry had an upper deck that was open. Both also had economy seats (similar to airplane seats), first class seating, smoking and non-smoking areas, which you specify when buying your tickets. Ferries of the conventional type have cabins which you can pay for if you wish. The loading and unloading is a bit of a madhouse as there's really no order to the process. Everyone is loaded on and off quite quickly though, so be on time (and be ready to get off at your departure island, the ferries stop at a lot of islands on the same route). That said, there's no "check-in" like at an airport.
A source of schedules of most ferry lines is www.gtp.gr , useful for a bit of pre-planning, however this can be wrong so best to contact the ferry agents on the islands, tickets can be bought online or bought from the ferry agents on any of the islands. Ferries can sell out during high season, so it is recommended that you purchase your tickets a couple days in advance.
