SFTP and FTPS are different, but both are secure.
SFTP is FTP over SSH (Secure Shell). The SSH is established and then the FTP login credentials are sent (never in the clear). The shell session(s) once established don’t require near the amount of overhead (handshaking) then straight FTP does, so the session is much more reliable.
FTPS is FTP with SSL (TLS) that is like an https connection (certificate with public/private key). Don’t know what certificate warning you are getting but, usually, it’s because the certificate was signed off by a known certificate authority (CA), might be expired or is self-signed. If the certificate is self-signed then you can around that.
between the two protocols, SFTP and FTPS are both very secure with strong authentication options. FTPS can be very difficult to patch through a tightly secured firewall since FTPS uses multiple port numbers.
Per the HostGator documentation, unless you are on windows shared plan, you should be able to use SFTP. You may have to change the port number depending on the plan.
In RapidWeaver publishing settings you change the port number by adding a colon
: followed by the port number to the FTP server name.