They missed one simple point - the financial district is above sea level.
The scope of plot expands:
U.S. reports plot to bomb NYC metro tunnels
FBI: Investigation of 8 al-Qaida operatives, 3 in custody, spans 6 countries
NEW YORK - Authorities have disrupted al-Qaida terrorists abroad who were plotting to attack the transportation tunnels running under the Hudson River between New York and New Jersey, the FBI announced Friday.
“For most of the year, we have been focusing on a group of al-Qaida followers who have targeted the Hudson River tubes,” FBI Assistant Director Mark Mershon said at a news conference. “We believe we intercepted this group early in their plotting and, in fact, the plan has largely been disrupted.”
Mershon said the plot “would have involved martyrdom, explosives and certain of the tubes that connect New Jersey with Lower Manhattan.” .....
http://www.msnbc.msn.com/id/13749418/
They may not have been able to flood Manhattan, but a bomb in the tunnel would set off a deadly chain of explosions trapping hundreds of commuters.