Thanks for all the input.

How does this sound?
Arrive into athens
Flight to Chania
Chania and western Crete for 5 days
Chania to Heraklion and Ferry to santorini
Santorini for 4 or 5 days
Santorini to Athens by ferry
Athens and NaFplio for 5 days

We might try to squeeze in Delos and Mykonos for a couple of nights if we think its not too tiring. But as of now this is the plan.
And travelerjan, as per ur suggestions, I think we will rent a car for a couple of days in Crete and try and see if we are comfortable with it. If we arent, we'll stick to public transport.

Also my parents are doing a turkey and greece package around the same dates and will be joining us at Athens for a few days. They are planning to do the Kusadasi - Samos (ferry) Samos - Mykonos - Santorini - Athens route Is this ideal? Or is there a route via Rhodes that they can do?