For the arguments, check the source:
$notify_message = apply_filters( 'comment_notification_text', $notify_message, $comment_id );
You have two parameters. The first is the notification text itself, prior modification by your filter. It is constructed earlier in the same function and is different for comments, trackbacks, and pingbacks. The second parameter, as you might guess from the name, is the comment ID. That is all correct, as per the Codex entry you found.
However, your problem is that only the first parameter is passed by default. If you want any of the others you have to ask for them by means of the fourth parameter of add_filter.
add_filter("comment_notification_text", "x99", 1, 2);
The third parameter is a priority. You can raise that or lower it depending on your needs. 1 should run your filter early.
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