In cases like this - its a good idea to ook your air and transfers through the cruise line - in most cases they will promise to get you to the ship no matter what happens.
But it has to booked through the cruise line itself (and it usually has a name, such as the "choice air program")
A travel agent can book it for you - but make sure they are clearly booking the cruise line's air program.
I am the editor, but I also speculate, ask questions and play devil's advocate. I reserve the right to change my mind.