The term “FTP with PGP” describes a workflow that combines the strong end-to-end encryption, integrity and signing of PGP with the FTP transfer protocol. While FTPS can and often should be used to protect your FTP credentials, the underlying protocol in FTP with PGP workflows is often just plain old FTP.
BEST PRACTICE: (If you like FTP with PGP.) FTP with PGP is fine as long as care is taken to protect the FTP username and password credentials while they are in transit. The easiest, most reliable and most interoperable way to protect FTP credentials is to use FTPS instead of non-secure FTP.
BEST PRACTICE: (If you want an alternative to FTP with PGP.) The AS1, AS2 and AS3 protocols all provide the same benefits of FTP over PGP, plus the benefit of a signed receipt to provide non-repudiation. Several vendors also have their own way to provide the same benefits of FTP with PGP without onerous key exchange, without a separate encrypt-in-transit step or with streaming encryption; ask your file transfer vendors what they offer as an alternative to FTP with PGP.