Yes. Since the IRS has the EIN for your LLC registered with your Social Security Number, you do well to list it so that it remains linked.
An LLC is considered a disregarded entity for tax purposes. This means that your filing status is not changed just because you have an LLC. You are still considered to be self-employed, and the income you receive self-employed is attributed to your personal tax return through Schedule C, whether the 1099 was reported to your Social or to your EIN.
Having said that, make sure that the company or organization paying you reports it to your EIN. The point of having it is so that your Social is used less for identification purposes, which serves as a protection for you.
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