Hook filter to change wp_upload_dir() path in multisite

Use the upload_dir filter.

add_filter( 'upload_dir', 'wpse_261931_upload_dir', 10, 1 );
function wpse_261931_upload_dir( array $uploads ) {
  if( is_multisite() ) {
    //* Do something interesting with the $uploads directory

  }
  return $uploads;
}