Looks like you have a single part message with uuencoded content. If the message was properly formatted with a Content-Transfer-Encoding header of "uuencode", JavaMail would decode it automatically for you. But it looks like it is not. You can decode it yourself using:
InputStream is = MimeUtility.decode(message.getInputStream(), "uuencode");
Then read the input stream to get the decoded data, e.g., to copy it to a file.