libraries_get_libraries should return an array of library directories, with the library name as the key and the directory as the value.
libraries_get_path will get you the path to a specific library (js).
Follwing your approach, this works fine for me:
$dir = "sites/all/libraries";
$files = file_scan_directory($dir, '/.*\.js$/');
I think it might be base_path that is breaking it in your example, as it adds a /
in front of the (relative) path from the site root.
Combining libraries_get_libraries with file_scan_directory will also get you libraries from profile and site specific directories:
$libraries_array = libraries_get_libraries();
foreach($libraries_array as $library => $directory) {
$files = file_scan_directory($directory, '/.*\.js$/');
$js_paths[$library] = $files;
}
dpm($js_paths);
It may be worth noting that these libraries may contain many javascript files that are not actually used by modules.