What about sticking a mild radiation field across the whole of NY...
wouldn't take to long to mod and would still allow people to do business and get the heck out of there.
It could be RP'd as either a terrorist act or as another Liberty "accident" like in the SP anomoly.
I know it would be harsh on new characters but it doesn't take long to get out of NY if you want to. Give them a few extra thousand on their start up money and it should cover them.
Also the bigger the ship the more expensive the repairs...