<font face="Verdana, Arial, Helvetica, sans-serif" size="2">Originally posted by Analise:
What was the FAA thinking when they granted CO permission to do that? 
I'm glad they now realize that such low flights might not be such a great idea in terms of dealing with fragile nerves. </font>
I doubt that they thought about it at all and almost certainly didn't grant any formal request ahead of time.
The most likely scenario is that the CO charter flight was inbound and during the new york approach call, they came in "with a request" and requested vfr sightseeing over a few landmarks at 3000. No procedural reason why that request shouldn't be granted.