In essence I agree with everyone and no one...at the same time.
A couple of generalized notes for everyone.
1. The area of WTC is currently not going to be open for new business it is instead getting a funky modern art/memorial thing built in its place (and it would be probably best to downplay that to keep emotions from running to high, imo)
2. Concrete deffinate locations work best, simply as this makes it where instead of saying something like "I own the XYZ club down the block" you can state "Traffic was murder getting from fifth and madison, up here took an half hour to go the block." creating a much more intresting intake.
3. Large landmarks should remains stable and where they are including Timesquare, Lady Liberty, et cetra.
Onto my opinions (yeah the above wasn't

)
I think it would be best if aliens were already intergrated to some extent into society (meaning the extistance and what have you), eventually someone is going to bring in a green three foot nut, expecting to be treated as normal. If aliens are accepted it will be easier for that to happen.
For a manmade diaster that would allow the alteration of a good part of NYC, currently in Canada certain scientists are working to capture lighting to power cities. Suppose the back up catchers for NYC overloads back shot during a minor tropical storm that hit Jersey, and the resulting oversurge of the grid would cause several fires, long term power outages are always associated with looting, pillaging...basically meaning you could demolish a good part of the city that way.
NYC is not near any tektonicplates (today), so earthrquakes in general wouldn't happen, and unless it was a colony ship (something in neighborhood of 400 Kilotons), that hit the surface in Maine, there wouldn't be enough impact to create a shockwave, let alone serious earthquake.
I suppose you could take a Deep Impact/Aramgeddon route and drop a large enough astroid near enough to NYC for it...but then why would prominat land marks remain umarked?
Hmmm...enough rambling for now...maybe more later.