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Does the Silmarillion have anything to say about this? I'll have to re-read.

Tolkein doesn't seem to have given a detailed origin for dragons, beyond their having been bred by Morgoth. The explanation in the video isn't entirely inconsistent with the legendarium; as a matter of policy Tolkein didn't want evil to be capable of independent creation, so orcs were originally twisted and tortured elves, trolls were corrupted ents, etc.

Glaurung and the rest of the first dragons, however, couldn't fly. That would seem to be a bit of a knock-out punch for the eagles theory. Ancalagon and his winged brethren wouldn't appear until centuries later, in the latter days of the first age.

Traditionally the answer to any unexplained creature of substantial power in Tolkein's works, Tom Bombadil excluded, has been that like the eagles, wizards, balrogs, etc. they were maiar of one kind or another.

I thought Tom Bombadil was one of the last Maiar in Middle Earth, at the time of the Fellowship. Am I thinking of a different tier of being?

It's probably a really good idea to open up the endlessly raging Bombadil controversy. Well so what, Tolkienian cosmology is fascinating. To some extent he's a deliberate enigma. Personally I favour the idea, if he's explicable at all, that he's the spirit of Arda itself or at least the foremost of a number of more provincial spirits. There are competing theories, but it's not really possible that he's a Maia.

Certainly there were any number of Maiar still knocking around at the time of the Fellowship: Gandalf, Saruman, et al; Sauron; Durin's Bane; Gwaihir; arguably Shelob (half-Maia at best); and depending on how widely you want to define 'in Middle Earth', Arien & Tilion (the bearers of the sun & moon), presumably Osse & Uinen, etc.

Bombadil calls himself, and the elves agree, 'eldest', and he claims to have been around before Melkor, who was definitively the first of the Ainur to descend into the circles of the world. He's unaffected by, and not really interested in, the Ring, unlike the Maiar who come into contact with it in the course of the story.

Ilúvatar set the Secret Fire, which gives sentient creatures their fëar or souls, burning at the heart of the world. I can't see an origin for Tom that doesn't derive directly from that, given that at the point he appears in the chronology there's very little else in existence.

I don't know what all this makes Goldberry.

Aha, Ainur, thank you! I knew I was probably thinking of the wrong term.

Either way, didn't know there was "raging controversy". I did however get to work on Lord of the Rings Online for 3 years, where I had daily access to one of the best lore-historians in the US( Chris Pierson, who sat next to me).

Pretty sure he said something along the lines of "One of the last in Middle earth that we know of", so there was definitely an open-ended element to the topic

Hey! Come merry dol! derry dol! My darling!
Light goes the weather-wind and the feathered starling.
Down along under Hill, shining in the sunlight,
Waiting on the doorstep for the cold starlight,
There my pretty lady is, River-woman's daughter,
Slender as the willow-wand, clearer than the water.
Old Tom Bombadil water-lilies bringing
Comes hopping home again. Can you hear him singing?
Hey! Come merry dol! derry dol! and merry-o!
Goldberry, Goldberry, merry yellow berry-o!
Poor old Willow-man, you tuck your roots away!
Tom's in a hurry now. Evening will follow day.
Tom's going home again water-lilies bringing.
Hey! Come derry dol! Can you hear me singing?