I'm a retired NYC area realtor and life long local resident. My first question - Did you sign an Exclusive Buyer Broker Agreement? If yes, it should have been explained to you how your real estate agent is being paid and from whom? Was your agent being paid by the seller? Did your real estate agent ever tell you that if the commission is below a specific percentage or dollar amount, that you would need to pay the difference? Read the document you signed because I'm sure you signed a broker agreement.
Next - read the lien notice. It needs to specify why the lien was placed. Don't guess or assume anything. It seems odd that your agent would put a lien on your home because of a commission dispute. Typically real estate agents want to be paid immediately - at the closing. If there was a difference / dispute with the commission fee, why didn't your agent call you, email you or file a civil lawsuit. Realtors pay for legal services and pay for Errors and Omissions insurance. This means for disputes like yours, the agent will contact their lawyer and ask to file a lawsuit. A lawsuit can be resolved a lot quicker than a lien.
In NYC, a lien on a home lasts for 1 year. If you don't sell the home within that year, the lien can disappear or the person can renew the lien. Why would a real estate agent wait an entire year with no guarantee that the lien will be resolved when all he / she has to do is call their lawyer and file a civil lawsuit?
To me, it seems there is more to this story than you know or stating in your question. Sounds fishy to me.