Well…

That depends on what situation you are talking about.

I mean if you are stressing the relative position of the airplane to the sea level, then "above" would be much preferable.

But it"s a tricky situation, as, in our common sense, all planes fly "above" the sea level.

According to English prepositions Explained, Above means that Subject(the plane) and Landmark(the sea) are not in contact.

In some movies, though, like pirates of the Caribbean 3, ships do travel below the surface of the sea…but, you get the idea.

In this specific case, my choice goes to "over", especially when the airplane is flying over the sea to its destination.

Otherwise, I get the idea that they are interchangable.

Hopefully you"ll find it helpful.

Updates

I"d highly recommend a book on English prepositions.

I find it immensely useful, when you get confused about the itsy-bisty, itty-bitty, teeny-weeny differences prepositions give you.

It take a while to get going, though.

You"re welcome to pick up my brains.

Pleasure to help.