Automotive Battery Disconnecting Safety
I would prefer to cut the negative (ground) lead - that way your tool will be at ground potential, and won't cause any additional sparks/fire hazard/excitement.  

If you cut the positive lead, and your tool touches the car body, it will make a short circuit between battery voltage and ground.

Even when disconnecting the battery in a non-emergency situation, disconnecting the grounded side first is recommended - disconnecting the positive side first may turn it into an emergency situation if the wrench happens to hit the car body!!