2 things...
Since the WOD in NYC is part of WDCo. not TDS you would think that they would get replenished before the stores since they are actually part of WDW. Most likely they were just out & the CM was confused/misspoke.
As a reminder, there is always a run on Disney Dollars before Easter/Spring Break times (combination of parents putting them in Easter baskets, senior trips & MANY, MANY people going to the world at this time) so if you need them soon I would start to stock up fast or you may not be able to get them until after Easter.