If your filing status is married filing jointly, on the screen where you enter Social Security benefits there are two columns, one for you and one for your wife. Enter the information from your wife's Form SSA-1099 in the column with her name at the top. This is for Social Security, not SSI.
SSI and Social Security are two different programs. SSI is Supplemental Security Income, not Social Security. As MindyB said, for SSI you do not get a 1099 form, and you do not report the benefits on your tax return. For Social Security you get a Form SSA-1099.
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