The best place at the end of the body tag, like
<html>
<head>
</head>
<body>
some html body tags
.
.
.
<script> external or inline </script>
</body>
</html>
If you do like so, then the html will load quicker and main pros is that all your ids and classes will get assigned otherwise sometime if you put script above html, then there might be a chance that you try to get an element by id that is not yet assigned in DOM
[UPDATE]
Here is an example code that Bootstrap is using in their own website: http://getbootstrap.com/getting-started/
you can find this code under Basic template Heading:
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->
<title>Bootstrap 101 Template</title>
<!-- Bootstrap -->
<link href="css/bootstrap.min.css" rel="stylesheet">
<!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries -->
<!-- WARNING: Respond.js doesn't work if you view the page via file:// -->
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<h1>Hello, world!</h1>
<!-- jQuery (necessary for Bootstrap's JavaScript plugins) -->
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
<!-- Include all compiled plugins (below), or include individual files as needed -->
<script src="js/bootstrap.min.js"></script>
</body>
</html>
