Cipher Configuration
Veracrypt lets you configure what ciphers and key lengths you’re using. This is beneficial to users who know exactly what they want.
Cryptomator uses the ciphers and configurations that are known to work well with each other. Our philosophy is slightly different here. We don’t want to give the user all the choices, we want to offer a software that is as easy as possible. Also our pre-chosen ciphersuite means less complexity and less attack surface. On the other hand if AES gets broken, we can not easily switch to let’s say Twofish without publishing a new release.
File Layout
Veracrypt creates just one container, so an attacker does not even know how many files you have.
Cryptomator encrypts each file for its own. While this enables cloud synchronization of just the files that really changed, it leaks the information how many files exist in a vault.
When to Use Which Software
I personally recommend Veracrypt to people who want to encrypt their USB flash drive and Cryptomator to people who want to synchronize encrypted files to some server.