I have seen articles (including NY times) that stated that the FDNY had the below companies on site between both 5th Alarms
112 Engine companies
58 Ladder companies
all 5 Rescue companies
7 Squad companies
4 Marine Units
+ All the Battalion Chiefs, Division Chiefs (at least 2), Staff chiefs and other special units
Per the 9/11 memorial, we know some of the companies that where there that lost a member:
9-11 Responder Memorial, We wanted to do something for the remembrance of all the first responders who lost their lives on September 11th 2001. This is a list of all the firefighters, EMS, chaplains, other personnel, members of private EMS and the fire patrol as well.
www.redlightsforfirefighters.com