This piece of history is related much more fully by the other evangelists, Matthew 14:23-33 Mark 6:46-52. See Poole on "Matthew 14:23", and following verses to Matthew 14:33. See Poole on "Mark 6:46", and following verses to Mark 6:52.
Related Commentaries of John 6:16
John 6:16
16 And when even was now come, his disciples went down unto the sea,