The income should be reported by the individual or business that provided the service and earned the income. If the 1099 is in your name, you could ask the issuing Company to change to the S-Corp if that is who earned the income. In the future, have a written agreement between your S-Corp and the Company you are providing service. Also, provide them with a Form W9, so they know where to report the 1099 income at year end.