1.Since there was no surname previously and youa re staying separately from your husband for long you can add your surname with that of your son.
2.So since the Municipality ahs refused to do so you can file a writ petition.
3.The courts have become much progressive nowadays and even while applying for passport the separated mother does not require signature of father of the child.
4.SO there is no reason why the court would not direct the Municipality to allow your surname with the name of your son.
Good luck.