You can decode base64 encoded email messages in Gmail, or files in your Google Drive, using the base64Decode() method of Google Apps Script.

function base64DecodeEmail() {
  // If the base6f.txt file in Drive needs to be decoded
  var mime = DriveApp.getFilesByName('base64.txt').next().getBlob().getDataAsString();

  // If a Gmail message with subject base64 needs to be decoded
  var message = GmailApp.search('subject:base64')[0].getMessages()[0];
  var mime = message.getRawContent();

  // Concatenate the chunks in the source
  mime = mime.replace(/\n|\r/g, '');

  // Extract the base64 string using regex
  var matches = mime.match(/base64[a-zA-Z0-9\+\/=]+/g);

  for (var line in matches) {
    var base64 = matches[line].replace(/^base64/, '');
    var decoded = Utilities.base64Decode(base64);
    var html = Utilities.newBlob(decoded).getDataAsString();
    Logger.log(html);
  }
}