I've turned down staying at the Milennium Hilton for a conference before now because I would find that view really disturbing. I know it's a memorial and many other people wouldn't feel the same about it though.
Do visit the Freedom Tower observatory if you can.
Imperial Blether- do not use Airbnb in NYC because short term lets of less than 30 days in the 5 boroughs are illegal. Also such sites never check the veracity of listings and people have been caught out. Would suggest you stay in a hotel instead because you will have some comeback if there are any problems.
The hotel is the W Downtown. There is an awesome nightclub bar in the lobby and everyone's gone Halloween crazy.
It's funny, because I come to NY Frequently and I've never been to Ground Zero or the memorial until today. We walked across it to get to Battery Park for Ellis Island and It was very moving. The Freedom Tower is fantastic, but if like me you're afraid of heights not a doer.
It was however the ideal opportunity to show DS 9 and explain what happened on 9/11.