It's probably not that simple. When the ship is in State waters, I assume that Florida law applies. I'd guess that the EO could apply until the ship exists Florida jurisdiction. I think that was the concept with the gambling cruises that would go offshore a few miles before land based casinos were allowed in FL.
I'm not sure how a port is governed with respect to Federal vs. State law. A State can't pass a law that says you don't need photo ID to board an aircraft but apparently they can require you to wear a mask in an airport.
Florida has no significant jurisdiction over the surrounding waters — that’s Federal (why we have the Coast Guard).
Ports involve overlapping jurisdiction between Federal authorities, State, application of International and Maritime law.
A governor can’t just step in with an EO.
Where the governor could try (and likely fail) to claim authority is on the argument that DCL has offices in Florida. And since they have offices in Florida, they can try to dictate conditions on DCL operations. But that argument will fail — Governor can’t just go disrupt interstate commerce with an EO.
The whole claim that he will apply the passport ban to cruise lines is empty virtue signaling.