I received my wife's 1099-G from Maryland. The boxes on the form and in Turbotax do not align. What state identification number do I use with state income tax withheld?

You can use their Federal ID number. Maryland Unemployment Insurance Department uses the same payer's identification number for Federal and State tax forms. The boxes on the Form 1099-G  don't always align with the boxes in tax software. Enter your information as present on your form to correlated boxes in TurboTax, it doesn't need to be the same box number.