Yes remove the Bonus.
NY is one of those states, like California, where they use 100% of your income to do their calculations. However, in the end it is usually just the income earned in NY that is actually taxed.
You can choose not to exclude some income. See the last choice.
Make sure you finish your non-resident state return prior to starting your residence or the credit for taxes paid to other states calculation will be problematic. make sure your home state return is last. Don't forget that income for dividend, interest, cap gains, should be removed from the NY column when doing the NY return as those income items are only resident state (exceptions may be for stock options earned income may be allocated to work state).
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