http://www.crete-holiday.org/crete-holiday-specials/

From Egypt to Crete on a ship?
I'm thinking of making this holiday a little special this year … I have an idea of spending a few days in Egypt with friends and then moving to Crete for the rest of my vacation. It is very easy to fly from Egypt to Crete, but I was thinking more of a boat trip from Alexandria to Chania or Heraklion. Does anyone know where I can get some information on prices, schedules, etc?
You will be able to do so, but may have to stop somewhere place and get a new boat, the more likely it is that Cyprus, which has a large cargo port of Limassol to vessels heading / going to / from Greece and to / from Egypt Israel or wherever. I'd better get a boat from Egypt to Limassol and contact a travel agent in Cyprus (before going) to set up your trip to Crete.