Tom has many names given to him. He was known as Iarwain Ben-adar to the elves; in Quenya this means Oldest and Fatherless. Forn was he called by dwarfs, and men called him Orald. Yet still even though all know of his existence no one can explain it. No one knows where he came from, what he is, how he lived for so long a time, or how he can control nature the way he does. Yet in the Fellowship of the Ring Tolkien leaves us clues to exactly what Tom Bombadil is, and where he came from.
"Eldest, that's what I am. Mark my words, my friends: Tom was here before the river and the trees; Tom remembers the first raindrop and the first acorn. He made paths before the Big People, and saw the Little People arriving. He was here before the Kings and the graves and the Barrow-wights. When the elves passed westward, Tom was here already, before the seas were bent. He knew the dark under the stars when it was fearless - before the Dark Lord came from Outside.”
The Fellowship of the Ring, “In the House of Tom Bombadil”
In the opening sentence Tom says that he is the "Eldest”. Now to be the oldest of all creation, he would have to be Eru himself, but this does not mean all of creation, rather of things living on Middle-earth. He was sent by Yavanna to watch over the forest, and to protect it. He was in the forest before the First of Men awoke, and before hobbits were around. He was already on Middle-earth before men built the Kingdoms of the North. Even before the Noldor Exile he was on Middle-earth. Leaving only the fact that he was a Maia, not one of the first humans to breathe. This explains his immortality and referring to him in The Silmarillion clearly states that.References: