Which is the best way to sync Obsidian: Syncthing or Cryptomator?

Cryptomator is not sync. It is just handling the on-disk encryption layer. You would still need a sync service to sync those encrypted files (syncthing or otherwise).

What devices you are trying to sync will determine what your options are. I don’t believe there is a way to use Cryptomator with iOS currently (for Obsidain).

Syncthing would be the way to go if iOS is in play (if thats what you’re after I will shill my own post here: Sync Mac/PC and iOS using Syncthing + Möbius Sync )

You could also go with the Obsidian Livesync plugin which offers some form of E2EE