I understand it's not safe to send passwords via email but when accounts are created via WHM/Cpanel, I have to let the user know what password I created for them. How can I relay the password safely?
Don't transmit a password at all. Set the password to something completely random, then automate a password reset. This will create a one-time link that allows them to log in, and forces them to change the password immediately.
Benefits of this scheme: