is there any passport control by ferry?by domestic flight

Once you are in the Schengen States of Europe, of which Italy and Greece are members, there is no passport control from one country to another. But because you are from the Philippines and are there on a visa someone might still ask to see your passport. I think it might be more likely to happen if you fly.

While technically there is no passport control, individual countries do have the right to ask to see your passport. If they do and see your visa has expired, you could be held and deported for visa violation.

Sorry to be so negative but those are the facts.

They always check passports in the airports. That's the only document you have regardless you have/need a visa.
I am certain that they don't check passports on ferries.