Bitvise has a great product called Tunnelier which can bridge FTP to SFTP. You could then use the standard FtpWebRequest in .NET.
http://www.bitvise.com/ftp-bridge
I am currently testing this for my own purposes and will update with my findings.
update
This idea is not ideal for unattended automation, unless you want to jump through hoops keeping the client connected as a service or something, which I accomplished by using NSSM.
I've tried CLI automation with various clients including bitvise and winscp.com. I've also tried these .net class libraries: Winscp, SSH.NET, SharpSSH, and the commercial SecureBlackBox SFTP client.
SecureBlackBox worked well, but it's very heavy-weight, can be quite expensive depending on the licensing, and I didn't agree so much with it's API.
Hands down, the best free sftp client for .NET development is winscp. I've written a few classes and extension methods to make working with it easier: Winscp.Extensions