If you're using s3cmd to put files into an s3 bucket and need to do so into GovCloud you can, but you need to override the end point URL's used for s3. I had a hard time finding documentation for this, so hopefully this saves someone sometime in the future.
s3cmd writes a configuration file, likely at ~/.s3cfg and in it are two options that you are not prompted for when going through the setup process, but are relevant when connecting to GovCloud. Specifically 'host_base' and 'host_bucket' need to be changed from the default s3 end points, they need to be set like so:
host_base = s3-us-gov-west-1.amazonaws.com
host_bucket = %(bucket)s.s3-us-gov-west-1.amazonaws.com
Once these are set your GovCloud access key and secret should work.