My son's user account and my user account on my iMac are linked/synced through iCloud. How do I unlink them?
On your sons account you should be able to open up System Preferences, choose iCloud (you should see your account logged in here). From there just click sign out. It will ask if you want to keep synced bookmarks, contacts, notes, etc you can then choose to delete them or keep them on that account.

Edit: Short answer: When you remove iCloud Drive from your sons account, your files will still remain on your account.
Longer answer: I tested out the iCloud Drive problem by creating a new user account managed by parental controls on my Mac. After I created this account, it asked me to sign into my Apple ID, which I did. I then went to sign myself out of the managed user account. I had the same thing occur, it said that my iCloud Drive documents will be deleted from this computer. I clicked delete, and removed them, as well as contacts, bookmarks, etc. When I logged back into my main (administrator) account all of my iCloud Drive files were still there, it is safe to delete iCloud Drive from that account.