I see quite a lot that speaks for Bombadil and Ungoliant being, if not truly opposed beings, at least of similar origin, but I do not see Eru in any way on the same level.
He has powers way beyond those of the other two. While Bombadil is Master in hiw own land, within the boundaries that he had set, Iluvatar is Master over all the creation.
A few quotes to support this thought:
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"But Rúmil said: 'Ilúvatar was the first beginning, and beyond that no wisdom of the Valar or of Eldar or of Men can go.' 'Who was Ilúvatar?' asked Eriol. 'Was he of the Gods?' 'Nay,' said Rúmil, 'that he was not, for he made them. Ilúvatar is the Lord for Always who dwells beyond the world; who made it and is not of it nor in it, but loves it.' " ~ BoLT, Music of the Ainu
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And also commenting on the "He is." part from FotR he says in a letter:
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As for Tom Bombadil, I really do think you are being too serious, besides missing the point. [...] You rather remind me of a Protestant relation who to me objected to the (modern) Catholic habit of calling priests Father, because the name father belonged only to the First Person.
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Pretty clear that Bombadil is not God and so in a way subordinated to Eru.