In the late 1970's, all the building-top helipads stopped operation after repeated accidents.
Still, there's the helipads along the river and a VFR corridor in and out of Manhattan. In 2009, the altitude rules for the corridor got a lot stricter because of repeated fatal accidents.
If you're a tour operator and want to use a city heliport, you need to sign a very restrictive agreement about operations, too-- which allows only limited overland stuff (e.g. flying over Yankee's Stadium/the Bronx). Mostly because people were sick of tourist helicopters constantly hovering over Central Park.
https://cityroom.blogs.nytimes.com/2010/04/30/rules-tightene...
None of this has anything directly to do with 9/11. Crashes of tourist helicopters and noise concerns has caused the city to clamp down on use of helipads. Crashes of air taxi operations in the 1970s caused the removal of the vast majority of helipads.
Both cities have plenty of potential even with overland banned. New York has a thriving helicopter business between boroughs, up and down both sides of Long Island and to and from the airports. The Bay Area isn’t similarly knitted together, but there is no good argument for not having an electric hop from e.g. Mountain View to SFO.
[1]: https://www.nydailynews.com/news/politics/new-york-elections...
I'm wondering if there's some context I'm missing.