A signing bonus is supposed to be reported on the w2 with your other income and is considered to be related to employment. You should answer yes, it is intent to earn money since it does have taxes due. Unfortunately, you will be paying your share plus the employer's share of Medicare and Social Security tax on the money.
You may want to contact the company and see if they can correct the situation since they are responsible for withholding taxes and clearly did not in sending you a 1099.
There is another option where you report the company and only pay your share. But as a new employee, I don't think you want to start by reporting them to the IRS.
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