It's my understanding that the ferries do go to a reduced winter schedule, though I don't know exactly when that kicks in. The major islands are still accessible year round, though they too may have limited schedules. I know for a fact that it can be difficult to get accommodations during the off-season (we went to Greece in March one year, and finally had to plan our itinerary around where we could find rooms, rather than the other way around). Borrow a couple of travel guides to Greece from the library, they'll have info about ferry schedules and accommodations, including those that shut down in the off-season.
There'll still be plenty to see and do in Greece, you just may have to be flexible about your plans.
And the weather should still be fairly decent, though you might not want to go swimming...