Assuming that the girlfriend was not a fugitive but only a runaway, the statute about harboring authorizes a $500 fine, up to 1 year in jail or a house of correction or pretrial probation with special conditions relating to the well being of the child.
Though it is unlikely that a near-in-age boyfriend would get the maximum penalty for a first offense, if there are aggravating factors such as a large age difference or sexual contacts, your son may still be in serious trouble.
Note: "It shall be a defense to a violation of clause (ii) if the defendant concealed or harbored a child in the reasonable good faith belief that the child would be at risk of physical or sexual abuse if the child returned to his custodial residence, unless the defendant concealed or harbored such child with intent to abuse the child or if the defendant committed abuse on that child."
Your son should hire a competent criminal defense attorney. Since harboring minors are handled in juvenile court, it would be a good idea for it to be a criminal defense attorney who is experienced in the juvenile court where the case will be heard. If he cannot afford an attorney, one will be appointed for him.
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Attorney Rich has covered the bases quite thoroughly for you. I will only add that you seek counsel early and have a chance to fully acquaint the attorney with the facts and circumstances. If you were assigned an attorney at the arraignment, call that attorney and schedule a few meeting between now and the next hearing date.
This answer is provided for informational purposes only and it is not intended as legal advice. Additionally, this answer does not create an attorney-client relationship. If you wish to obtain legal advice specific to your case, please consult with a local attorney