If your son has been in NY State for 6 months, a NY court has jurisdiction over custody. I would recommend that you meet with an attorney as soon as possible to discuss filing in Family Court to prevent her from taking your son to Germany.
Obtain a court order through an attorney to prevent her taking the child out of the country without a relocation hearing, assuming NY has jurisdiction through adequate residency of the child. There are also one or two treaties or international compacts that come into play, reinforcing you need of an attorney, but you should act quickly.
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You should file for custody immediately in order to get the courts involved. Even if you obtain a visitation order it would make it extremely difficult for her to soirit your child out of the country without your permission. Good luck.
I have been a criminal attorney in New York for almost 25 years. website: Brooklynlaw.net Phone #: 718-208-6094 email: firstname.lastname@example.org. This answer is only for informational purposes and is not meant as legal advice.
You should file a petition in Family Court for custody claiming that your wife is seeking to interfere with the father/child relationship. International law does not play into this since your aim is to keep your child here so long as you act right away. Best defense is an offense.