Recently terminated from my sales job. Can an employer withold commissions earned through the date of separation?

No.  The New York labor law makes it a very serious offense for an employer to withhold compensation which is due and owing.  Depending on the particular facts and circumstances, the employer could become liable to pay not only the owed compensation, but also attorneys' fees incurred in collecting the money and a possible 25% penalty.  Of course, I've practiced law long enough to know that the employes is going to claim that it doesn't owe you the money.