I dont know how informative this is, but I just had a big scroll through a NYC finalised report (alongside Manhattan Dispatch) and found at least these cars responded:
Car 1 - Commissioner
Car 2 - 1st Deputy Commissioner
Car 3 - Chief of Department
Car 4 - Chief of Operations
Car 4B - AC of Operations??
Car 4C - DAC of Operations??
Car 4D - DAC of Operations??
Car 4E - DAC of Operations??
Car 4P - Chief of Planning
Car 5 - Unknown
Car 9 - Unknown
Car 9C - Unknown
Car 9D - Unknown
Car 33B - Unknown
Car 40A - Unknown (Chief of Rescue Ops?)
Car 40B - Unknown (Chief of Hazmat Ops?)
Car 40C - Unknown (Chief of Marine Ops?)
Car 6 - Chief of EMS
Car 6A - Assistant Chief of EMS
Car 6C - Tour 1 EMS Chief Officer (Unsure of it's actual role - CO was simply it's description on a report)
Car 63 - EMS Division 3 Chief
Car 64 - EMS Division 4 Chief
Car 65 - EMS Division 5 Chief
Car 621 - EMS Division 2 Deputy Chief
Car 661 - EMS Division 6 Deputy Chief
There were obviously more which I haven't found, but this list I've found so far which I can confirm from radio tapes, or FDNY reports.
Those with a '??' is simply assumed based off of current roles. I strongly suspect the car 40's are what the car 11's are now - based off of how '40C' early on says that all the boats are available in the river and a comment regarding rescue relocations from '40A'. (If this is true: C40A is Rescue Operations, C40B is Hazmat Operations, C40C is Marine Operations).