I have a 6mth old boy, not sure if I am his father. I have estranged myself from his mother, who threatens to harm him, or she will go out drinking and drive with him in the car etc. What rights do I have as his father, and could I possibly go for custody if my name is not on his birth certificate?

I would consult a local family law attorney. You might also find this site helpful:
Custody Fathers Rights - Be Prepared! | Fathers Speak - New Zealand

You will need to go to your local Family Court and file a petition for custody. This will probably require a paternity test to make sure you are the bio father. From there the court will determine legal and physical custody as well as visitation and support.