Re: Greek cruise
I think you should start with the places you can fly in and work from there. Since you would like to cruise both the Aegen and Ionian Seas I would say Aegina would be a good spot. Easy access to Athens and placed between both the Aegen and Ionian islands though you would have to go the canal for the Ionian islands.
Ithaca has a well protected harbour and I recall seeing a few boats on the hard. At the other end Rhodes and Kos have a marinas.
If going through the canal Itea has a fairly new marina and you can catch a bus to Delphi
Hope that helps.