Seems pretty solid but it's hard to consider balance at higher challenge ratings. Have you considered less challenging variants, or a wider leap in power in your variants for lower level encounters? Or are these exclusively big-baddies?
I would say 3d6 damage (30ft falling) then however much damage the boulder does. Dex save for half, or possibly becoming trapped underneath. It's really up to you but the suggestions here are solid.
A wild bard college appears!
But yeah, I'd allow that beholder. It's well done! If I were to change anything, I might address how the runt beholders fit in an adventuring party. How does the beholder sell the loot from his adventures? Does he sleep at the inn? Are there illusionary spells employed?