OK. You are correct. Rent Stabilization does not allow for a roommate to be charged more than a proportionate share of the rent.
A prime tenant exposed to the landlord for overcharging the roommate may face an eviction proceeding.
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The answer provided to you is in the nature of general information. The general proposition being that you should try to avoid a bad outcome if you can.
Speak with him about this first and maybe he will give you some money back. If talking about it does not work, then it may be time to consult with a New York landlord-tenant attorney regarding your rights and/or remedies.
First you need to discuss the facts of your claim with an attorney. The next step would be to have that attorney engage the individual/s in an attempt to obtain some form of retribution. If that fails legal action may be required. The first step for you is to speak with an attorney, my firm handles these types of cases in NY.
Law Offices of Nicklaus Misiti
212 537 4407
Legal disclaimer: The statement above is general in nature, as not all the facts are known. You should retain an attorney to review all the facts specific to your case in order to receive advise specific to your case. The statement above does not create an attorney/client relationship.
You may want to file an overcharge complaint with DHCR. If the roommate is the primary tenant you may be entitled to treble damages if the primary tenant charged you more than 1/2 rent (if you shared with only the primary tenant) plus 10% if the apartment was furnished.