I've worked hurricanes in the South and I would assume that your area water will be treated much the same. They have federal guidelines to follow on health. Keep in mind that the health department may be busy but they are still doing their jobs. They are also drinking the same water as everybody else. They are not out to poison folks.
What that means is the guys taking the water samples all around the system and sending them in for testing are still there. If the testing comes back that the water is bad, they put out the word not to drink the water. Heard of any boil water orders for your system? If not, the water is safe.
If the water smells like chlorine, it is because the test shows more is needed but it still will be within the safe limits and Prime, etc. is sure to handle it. If there is some sediment in the tap it is just logical that the pipes got a pretty good shaking. If you've got trees, cars, and houses floating around, is there any reason a bit of rust won't come off the inside of the pipes?
The water may look funny or smell funny but it is safe if they have not said otherwise. That rust is the same rust that the water runs through every day. It's just loose and coming to your house to stop up those little screens on faucets!
This is just a routine hurricane except that it is New YORK instead of New ORLEANS.
No better, no worse if you are ready for it.