I am struggling to find an FTPES ( Must be explicit ) FTPS with a Java Client API. I have an FTPS server that needs a CA certificate as well as username and password. Now I can do this with something like SmartFTp or Curl which allows me to have a client side certificate check. I had a look at a Java binding for Curl - that could be an option but I'd rather use a direct API client library.
I've used the edtFTPPro/J commercial library for SFTP/FTP, and it works really good. Also supports FTPS, and at least for SFTP, you can use your own certificates. Haven't used it for FTPS, but I'd expect it to work fine. They also have very good response times on their forums.