The link throughput takes into account the entire traffic that was sent through the link. It includes data packets and control packets and includes retransmission's, errors or collisions. This would also include packet flows from multiple applications that may flow through the same link. Also note that the packet size at the link (physical layer) is the packet size at the application layer plus overheads added by different layers in the stack.
The application throughput only takes into account those data packets (application layer packet size) that were sent from the source and that were successfully received at the destination.