In NYC, the protections for pregnant workers are very strong. It will be a huge mistake for your company to let you go while you are out on short term disability (STD). If they do, consult the NYC Commission on Human Rights, or a lawyer.
You may still be due a reasonable accommodation for your pregnancy, I would suggest scheduling a free consultation with an experienced employment attorney immediately.
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While employers generally can fire employees who happen to be pregnant, they cannot fire you because you are pregnant. I would recommend you talk to an employment lawyer about the specific facts of your situation.
My answer is based on the limited information provided in the question, and should not be considered legal advice. If you are looking for legal advice, you should contact an employment attorney. The Nirenberg Law Firm, LLC represents employees in New Jersey and New York. Please feel free to call us at (201) 487-2700.