To file as head of household, you must live apart from your spouse for all of the last 6 months of the tax year (from July 1 to the end of the year), you must provide care in your home for at least one qualifying dependent, usually your own child, and you must pay more than half the cost of maintaining the home where you live with that qualifying dependent.
Whether you are legally separated on the way to a divorce, or living apart for other reasons (military deployment, incarceration) does not matter for the head of household rule.
If you do not have a qualifying dependent, you should update your W4 to single but expect to file under "married filing separately." The tax code says that if you are still married, you can file as single if you are "considered unmarried", and to be "considered unmarried", you must either meet the definition for head of household, or you must be:
Legally separated from your spouse under a divorce or separate maintenance decree. (State law governs whether you are married or legally separated under a divorce or separate maintenance decree.)
The problem is that most separations, including New York, do not qualify under this rule. While a court may have approved your separation or be supervising it, it is not a legally binding decree under NY law. The only way to get a legally binding decree under NY state law is to go all the way to the end of the divorce proceeding but make it a binding separation instead of a divorce. Since it costs as much money and is as difficult as a full divorce, no one does it for practical purposes. As a result, separations in NY do not meet the IRS test for being "considered unmarried" that would allow you to file as single.
Married filing separately can have some disadvantages. You will probably be better off financially if you can finalize the divorce before December 31, 2016. (Assuming there is no chance of reconciliation, of course.)