Under New York’s Vehicle and Traffic Law Section 1117, motorists approaching a mal-functioning traffic light should stop their vehicles as if they are approaching a stop sign. This means come to a full stop. The only exception is when a police officer directs you to proceed otherwise.
Once stopped, you must obey the applicable right-of-way laws. Specifically, under Vehicle and Traffic Law Section 1142, following your stop, you must yield to any other vehicle that has already entered the intersection from any other direction or one that presents an immediate hazard.
A malfunctioning traffic light creates an extremely dangerous situation. You should always proceed with extreme caution. Also, keep in mind that emergency conditions do not allow you to ignore the traffic laws. Police officers will stop you and issue you a traffic ticket even in such conditions.
Drive safe out there!