A Jew is not allowed to do something for no purpose, so they would only be allowed to board the ship in the first place if there were a purpose – such as attaining the menuchas hanefesh (peace of mind) and simchas hachaim (joy in life) needed to be ovdei Hashem and to be able to learn b’hasmada (with diligence).
If their boarding as a purpose for their avodas Hashem, that would override any pollution concerns (assuming they are doing nothing that is illegal or unusual).