From https://wpxtre.me/blog/tips/standardize-issue-labels-between-your-github-repos/#.VE9mjvSsV1M

github_sync_labels.php

<?php

// credential to access github, you should choose between username/password authentication or token (for two step verification accounts)
$githubUser         = 'YOURGITHUBUSER';
$githubPasswd       = 'YOURGITHUBPASSWD';
// or
//$githubToken        = 'YOURGITHUBTOKEN';

$githubOrganization = 'YOURGITHUBORGANIZATION';

// the list of repo in your github organization you want to align
$repos = array(
  'YOURREPO#1',
  'YOURREPO#2',
  'YOURREPO#3',
  // ...
);

// Add, remove, or set names and colors of issue labels as you wish
$arrayLabels = [
  'a:docs' => 'c7def8',
  'a:design' => 'c7def8',
  'a:sysops' => 'c7def8',
  'a:customer' => 'c7def8',
  'e:1' => 'd4c5f9',
  'e:2' => 'd4c5f9',
  'e:3' => 'd4c5f9',
  'p:blocker' => 'e11d21',
  'p:high' => 'f7c6c7',
  'p:normal' => 'f7c6c7',
  'p:low' => 'f7c6c7',
  's:in-process' => 'fef2c0',
  's:needs-discussion' => 'fbca04',
  't:bug' => 'bfe5bf',
  't:idea' => 'bfe5bf',
  't:support' => 'bfe5bf',
  't:feature' => 'bfe5bf',
  't:question' => 'bfe5bf',
  't:refactor' => 'bfe5bf',
  't:improvement' => 'bfe5bf',
  't:discussion' => 'bfe5bf'
];

$arrayMilestones = [
  [
    'title' => 'Next Iteration',
    'description' => 'What are we doing right now?'
  ],
  [
    'title' => 'Next Tasks',
    'description' => 'What we are not doing right now? but we will probably do soon'
  ],
  [
    'title' => 'Blue Sky',
    'description' => 'What we are not doing right now? but we will probably will not do soon'
  ]
];

foreach( $repos as $repo ) {
  foreach( $arrayMilestones as $milestone ) {
    $milestoneToSet = '\'{ "title": "' . $milestone['title'] .'","description": "' . $milestone['description'] . '" }\'';
    if (isset($githubToken)) {
      system( 'curl -u ' . $githubToken . ':x-oauth-basic https://api.github.com/repos/' . $githubOrganization . '/' . $repo . '/milestones -X POST --data ' . $milestoneToSet );
    } else {
      system( 'curl -u "' . $githubUser . ':' . $githubPasswd . '" https://api.github.com/repos/' . $githubOrganization . '/' . $repo . '/milestones -X POST --data ' . $milestoneToSet );
    }
  }

  foreach( $arrayLabels as $name => $color ) {
    $labelToSet = '\'{ "name": "' . $name .'","color": "' . $color . '" }\'';
    if (isset($githubToken)) {
      system( 'curl -u ' . $githubToken . ':x-oauth-basic https://api.github.com/repos/' . $githubOrganization . '/' . $repo . '/labels -X POST --data ' . $labelToSet );
    } else {
      system( 'curl -u "' . $githubUser . ':' . $githubPasswd . '" https://api.github.com/repos/' . $githubOrganization . '/' . $repo . '/labels -X POST --data ' . $labelToSet );
    }
  }
}

Added support to milestones