Im in training for the NYC Marathon. I am taking 1 minute walk breaks. I would like to know if I count them into my long runs?? Today I ran 18m, but with walk breaks I had to run 2miles more because i didn't count the walk breaks. What is the best way to do this? Count it, or Not??

Count them!
Once the start horn goes you're on the clock until the finish line. If you need them, take them but as a suggestion tie them in at water breaks to ensure you're getting the max value from the break by getting a break and ensuring you're allowing yourself take onboard food/drink. Running and drinking from a cup is all but impossible.