It is not clear from your question what your options are. What does this "harassment" consist of? Threats? Stalking? Or just being a nuisance because you don't get along?
If the "harassment" is truly frightening or extremely annoying (odd hours of the night, perhaps the showing up at your job, repeated telephone calls), you might be able to get an order of protection, and if the behavior persists, seek police intervention or court contempt/violation proceedings.
I take it you have de facto physical custody of your son because the mother has so far "abandoned" him to your care, but have not gone to court yet to establish that you have legal or physical custody and some sort of shared parenting plan or schedule for the mother to have visitation or shared parenting? I would certainly consider doing this as soon as possible, and looking into a Family Law attorney in Onondaga County to assist you.
Getting court ordered and approved arrangements may help to stop or moderate this harassing behavior of the child's mother you are complaining about.
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If you feel threatened in any way, file for an order of protection, however it is a far-reaching document that is not meant to be requested unless there is a serious threat of danger.
You would appear to have a basis for the harassment charge. As to whether you may withhold access to the child, this involves an assessment of the prior orders (if any) & more details regarding the situation. Thus, you should consult a Family Law attorney in your area.
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