Being the resource-rich metropolis that it is, NYC has a wealth of mapping resources of all varieties. Below are links to several good places to start and a special section on September 11.
The New York City Map Portal provides you with access to New York City data and NYC.gov applications with address level data and maps. Find building, property, and community information as well as neighborhood statistics with ease.
The Center for Urban Research at CUNY works with city agencies, non-profits and others to provide access to and analyze data about New York. They have produced (among other fantastic resources) the websites 1940s New York, Redistricting and You, Changing NYC Neighborhoods, and the major resource OASIS (the Open Accessible Space Information System).
NYC OpenData supplies many sets of public data produced by City agencies and other City organizations.
The NYC Department of City Planning's data page, called BYTES of the Big Apple, has a number of layers of data and other files, most of which are free.
The Virtual Terrain Project maintains an extensive (and opinionated) web site index to map and data resources for New York State and locations within the state, including extensive NYC sites and a special section on the World Trade Center.
Thirty-two historical maps of New York City from 1776 to 1918 are now available for viewing as a special collection within the David Rumsey Map Collection. You will need to install a free browser plugin to view these maps.
Here's an index of (mostly) historical maps of New York State maintained by the Stony Brook University Map Library.
The New York State Museum offers many layers of map data on its GIS Datasets page.
The Museum of the City of New York presents Mapping Staten Island in conjunction with the exhibition "From Farm to City: Staten Island, 1661-2012."
The New York Public Library's Maps Division developed the Map Warper, an online tool that allows the easy alignment of historical (mostly fire insurance) and digital maps. This alignment allows one to connect historical maps to many other sources of data to further the analysis of the history of New York City.
If you are feeling technically-inclined, you can read an article on the new New York City Base Map to learn what digital cartography is like these days.
The September 11 Digital Archive uses electronic media to collect and present the history of the attacks.
Not a map service, but a worthy resource nonetheless, the 9-11 Oral History Project from the Columbia University Libraries consists of five projects and programs focusing on different areas of inquiry related to the aftermath of the destruction of the World Trade Center.
GeoCommunity maintains a page of The Geospatial Industry's Response To Terrorism.
A wonderful resource for all kinds of maps, the Perry-Castenada Map Collection at UT-Austin has a special collection of September 11th-related maps.
The Library of Congress maintains a special page of September 11th-related acquisitions called Witness and Response, including the Geography and Map Division.
The Smithsonian Institute also has a number of maps related to September 11th at their web site, Bearing Witness to History.
Find architectural information and photographs of the World Trade Center at Great Buildings Online.