Yes, it does it by simple order, and by default ssh-dss is listed first. You can change the order in SSHFTPClient like this:
sshFTP.disableAllAlgorithms(SSHFTPAlgorithm.KEY_PAIR);
sshFTP.setAlgorithmEnabled(SSHFTPAlgorithm.KEY_RSA, true);
sshFTP.setAlgorithmEnabled(SSHFTPAlgorithm.KEY_DSA, true);
This puts them in the order ssh-rsa,ssh-dss.