According to the WordPress Shortcode API documentation, the first parameter can be used to accept the shortcode attributes.
You can reconfigure your function like so:
function slider_func( $atts ) {
extract( shortcode_atts( array(
'width' => '600', // default width
'height' => '400', // default height
), $atts ) );
?>
<script>
jQuery(document).ready(function($) {
$('#banner-fade').bjqs({
height: <?php echo (int) $height; ?>,
width: <?php echo (int) $width; ?>,
responsive: true
});
});
</script>
<?php
}