Ive used the free version of PRTG to do more so real time graphs in the past.
Of course, you could also whip up a script that uses RRD tool to do the same thing for free.
PRTG is also a Windows based tool which may or may not be useful (which is also the reason why I wouldnt use it more extensively than the occasional exercise.)
But you are right. If you download 50mbit/sec for only a couple of seconds, you probably wont see it on your 5 minute averaged graph.
You need to download full speed for 10 minutes, or enough to cover 2 polling periods to get an accurate figure.