Filezilla is the best hands down, and I will extrapolate on why if I have to later on. I have used many, but it supports SFTP, which is what you want - never use FTP it is not secure.
It also displays the commands while you are in your remote server so you can see what is going on, is fully POSIX compliant with it's permissions configuration tool, and works on every platform. So, if you ever switch to Unix, Linux, Mac OS X from Windows you can still use Filezilla.