I can actually confirm this as I heard from multiple sources. As a matter of fact the Twin Towers were originally set to be the setting for the final boss. Also they played a prominent role in the real ending of the game which has Thor cameo appearing at the ending after Spider-Man defeats Electro. Thats the reason why the newspaper claims that Thor defeated Electro at the final ending and Spidey gets mad for not getting any credit. The Twin Towers were in the background of some of the levels, including the the final battle with Electro strangely enough. They were removed in post 9/11 copies however the FMV which explains the true ending with Thor involved had to be cut completely due to not being able to have the Twin Towers taking out. The sources are there I'm just too lazy to find them
