I was hired to work for a new company. He took income tax out of my checks. Now he sent me a 1099-NEC instead of a W 2. What should I do? I am no longer working there.

The first step is to contact your employer. 

• Simply question why you got a 1099-NEC instead of a W-2. .
• Do you have any kind of of pay stub that can confirm that taxes had been taken out.
• Be sure that you are correct before going further.

If you are convinced that taxes were taken out,  your next step is to contact the IRS.

• You can call toll-free at 1-800-829-1040 or visit a Taxpayer Assistance Center Local IRS Office .
• IRS will send your employer a letter instructing them to issue a corrected version within 10 days.
• You can file your tax return reporting what you think is the correct amount of wages and withholding using Form 4852, the "Substitute for Form W-2".
• The IRS will advise you of this option when you reach out to them. You'll have to reference your pay stubs if you use this form.

A Form 1099-NEC can report income tax withholding, so if the Form 1099-NEC shows what was withheld, there is no problem (as long as the company actually sent the withheld income tax to the Treasury).  If the company withheld Social Security and Medicare taxes as well, they apparently considered you to be an employee and should have sent you a W-2, not a Form 1099-NEC.  It's not legal for them to simply withhold taxes and keep the money.

The more basic question is whether or not you were an independent contractor or an employee under the law:

https://www.irs.gov/businesses/small-businesses-self-employed/independent-contractor-self-employed-or-employee