I think Tom Bombadil was a manifestation of Eru (Iluvatar). When Frodo, Sam, Merry and Pippin are invited to have a meal with Tom and Goldberry, Frodo asks her, "Who is Tom Bombadil?". She answers, "He is". This is exactly what 'Eru' means and so I think this is a hint to the origin of Tom Bombadil.
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