JSch supports SSH subsystems in general but does not implement anything NETCONF specific (this is not necessary).
All you need to do is to make the following calls (pseudo-code):
com.jcraft.jsch.JSch ssh = new com.jcraft.jsch.JSch();
com.jcraft.jsch.Session session = ssh.getSession(username, host, port);
session.setUserInfo(myUserInfo); // authentication
session.connect(connectTimeout);
// this opens up the proper subsystem for NETCONF
com.jcraft.jsch.ChannelSubsystem subsystem = (com.jcraft.jsch.ChannelSubsystem) session.openChannel("subsystem");
subsystem.setSubsystem("netconf");
// at this point you may get your streams
subsystem.getInputStream();
subsystem.getErrStream();
subsystem.getOutputStream();
subsystem.connect();
For NETCONF, the only requirement that the subsystem has to fulfill is a proper subsystem name.