If you're going to start "thinking" this or that part of the Bible is just a story, then you're going to be on very shaky ground indeed. How are you going to know what to believe?
All the creatures of the earth were not on the ark. Two of each were, and seven, I believe, of sacrificial animals (could be wrong there).
We tend to limit God, but if it was His will to save Noah's family and all of those animals, and it was, then it was perfectly possible. Think of it this way....the greatest miracle of all, His creation of the heavens and the earth, had already happened. From there, it's a small thing indeed to shut some animals up in a boat.
Thanks.