The great and terrible tempest didn't stop when Laman and Lemuel untied Nephi, although that was certainly necessary. It stopped after Nephi prayed unto the Lord:
In one instance, Nephi prayed to the Lord, Jehovah, the premortal Jesus Christ, to stop the tempest. In the other instance, the mortal Jesus Christ rebuked the tempest directly. In both cases, it was the same person, the same power, that controlled the elements: the Creator of the earth, the God of nature.