Tom Bombadil had the power to overcome them, but he certainly didn't set the Barrow-wights after Frodo and the Hobbits; that fact makes Bombadil not their commander.
The Witch-king of Angmar probably commanded the Barrow-wights, since he was the one who sent them to the Barrow-downs in the first place, during the wars with Arnor.
Of course, it could also be possible that the Barrow-wights commanded themselves. Angmar did vanish from the world, and they were evil spirits, and by definition, evil usually involves doing harm and creating chaos. But I think that theory is delving too deep and getting too far-fetched.
There's just my logical, deductive two-cents on the matter. (Sorry, once I get thinking, I grab the topic and run.)
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"The fires of Isengard will spread, and the woods of Tookborough and Buckland will burn, and...and all that was once green and good in this world will be gone! There won't be a Shire, Pippin." ~ Merry, TTT
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