It will be tight but doable, assuming you don't have to wait to get the license. I've heard horror stories about that aspect of the process in NYC to the point that we got our wedding license up-state the Friday prior to our wedding rather than doing it in advance at city hall. Basically the three hour window you've given yourself depends on no lines at any point in the process. On the plus side, it is going to make a great story! Oh, and you will most likely have the full SSSS treatment getting back on the helicopter, so figure you need 10 minutes for that to happen.
Assuming that you're at EWR at 17:10 you'll have no problem boarding the flight to BRU on time.
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And I would definitely come out to watch the race between sites (and help if necessary) if you shared the date.