The only way to do this in a semi-secure manner is to have apache use mod rewrite to act as the front end for everything and never pass the user off to the NT server directly, or to map a drive to the NT server that holds the data.
If you can map a drive to the NT server, that would be the easiest way.
If you've got a lot of fine grained permissions that have to be served through IIS, then you can pass people off with something like this:
$auth = $PHP_AUTH_USER . ":" . $PHP_AUTH_PW;
print "http://$auth@yourserver.com?somefile.html";
Not at all secure, but it should work