My car was listed as totaled by the ins co and I was told it would be "a while"
Before it can be towed away.

My area was flooded by Sandy. She told me
To take off the plates and leave the key in the car. I kind of laughed at that
Because I live in NY and you don't leave keys in the car. Also, without
Plates I'm afraid the city might take the car, then I won't get my ins
Settlement. My ins co did put their co name on the windows in felt pen
And wrote TO which I guess means totaled.

She said they will only give me a one hour warning when they come to tow
And if I'm not home they will tow it with the plates. I'm also afraid of
Alternate side parking tickets. She didn't know what to say.
Any advice would be welcomed.

Put a sign in the window indicating the car is inoperable due to damage from Sandy and is awaiting tow by the insurer. Include the insurer's name and a claim #.

Sorry to hear that folks are receiving such shoddy service. Is there any possibility that the city (county ? State?) would honor a cardboard replica of the plate in front and back windows, plus the info Scott suggested and maybe phone number. Have you talked to police to see if they have any policy for these emergency conditions?
I wouldn't trust this company to follow through with the one hour notice myself. Tow drivers may just chuckle at that requirement. Could you have it towed to a location specified by the insurance company yourself? I would be looking to protect my investment here even if it cost me some bucks. Also get a very specific receipt. Stealing these cars, laundering titles and selling the cars with no notification that they are flood damaged may be a popular scam right now.
Good luck with all this. This could easily be me instead of you. We were in the bullseye all along for Sandy but got lucky at the last moment.