Well, Autoloader could work nicely with the notification event for arriving files. You could probably specify a window duration for your "on-time" arrivels and that could be your base check for on time. As files arrive they go to their window and when the file metadata is ingested with Autoloader, you compare the arrival time to the window + the late watermark.  You could trigger alerts for files that come in past the watermark. 

I guess some of this would depend on the on-time vs late being a regularly scheduled thing.