This could also translate to 'Is our ship running late?'
It could just be translated to "Is our ship late?", because whether or not you add "running", the sentence means the same.
That is true, of course.
It was not a question. :)
Sorry, I misread the question mark outside the quotes...
"Is our ship late?" should be accepted. It is what native speakers say. Also, if the ship is delayed, it raises the question what caused the delay.