State tax filing

You should not delete the W-2 for box 16 for Massachusetts.  The state just does not allow efiling when there are multiple W-2s.

Since you are a resident of MA all income earned in NY will be taxed in MA and NY. You will need to file a non-resident return for NY and a resident for MA. To ensure accurate calculations, always complete the non-resident (NY) return first because your resident state (MA) will give you a credit for taxes paid. 

As a Massachusetts resident, all wages earned are taxable to Massachusetts. When a Massachusetts resident works out of state, those wages are still taxable to Massachusetts. Some employers will list on Form W-2, Box 16 the amount that is taxable to the state where the wages were earned and will also report the amount of wages that are taxable to Massachusetts, due to the employee's state of residency. Typically there is withholding reported for both states in this situation. This becomes an issue for residents using MA Form 1 because the amount of taxable wages is often greater than it should be. This occurs because Massachusetts residents are taxed on all wages, regardless of which state they are earned in. Because the wages were listed twice on the W-2, they are now also listed twice on MA Form 1. 

One option is to request a corrected W=2 showing only the amounts in Box 16 attributable to the State in which they are earned, and not to each state for which the wages are taxable. This will be difficult to obtain so you may have to paper file your MA return. 

See the link below for other options:

Same State Income 

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