It is not necessarily to clear custom at a “Port of Entry” when arriving to Greece, from Turkey or other country outside Schengen.
All you need is a Greek Entry Form and a Hellenic Coastguard office, Port Authority. I guess another requirement is a local police office.
You can download the Greek Entry Form here.
As you can see you are supposed to call up the Hellenic Coastguard and ask for permission to enter the harbor. This was something we did not do!
At arrival you visit the Port Authority with the form passports and people onboard. Port Authority will check identity of the people against the passports before they sign and stamp the entry form. After that it is time to visit the local Police station for a second stamp.
The form should be returned to the authorities when you leave Greece. We used this form when returning to Lakki, Greece from Turkey. Instead of clearing in Kos we decided to go directly to Lakki as it would save us one day. Port Authority and the local Police acted like it was the first time they had seen the Greek Entry Form. After some telephone calls, they accepted the form and gave us the stamps.