Yes, an individual in removal proceedings is eligible to apply for a J-1 waiver, but I do not recommend trying to navigate that process on your own. Filing a waiver and convincing the Judge to continue the case long enough to receive a J-1 waiver approval can be quite complicated. I recommend that you consult with an Immigration attorney as soon as possible to ensure correct and timely filing of your waiver application.
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USCIS has jurisdiction over he waivers.
NYC EXPERIENCED IMMIGRATION ATTORNEYS www.myattorneyusa.com; email: email@example.com; Phone: (866) 456-8654; Fax: 212-964-0440; Cell: 212-202-0325. The information contained in this answer is provided for informational purposes only, and should not be construed as legal advice on any subject matter.