The Form you are referring to "Instructions for Forms IT-260 and IT-260.1 Change of Resident Status — Special Accruals"
is addressing a change from being a New York CITY resident and income "earned" but not yet received.
You say- "The second paragraph seems to indicate the final two paychecks are considered from New York but the bonuses aren't since the amounts weren't predetermined"
I suggest you ask the former employer about that, but the instructions states "determinable at or before the date of the change of residence", so not necessarily "predetermined".
I assume the bonus was calculated on the employee's performance which was done before leaving the job (before becoming a non-resident) so I assume the bonus could have been determined before your move took place.
The amount of the paychecks would be both New York State and New York City income.
The Bonus most probably is also New York City taxable income since there most likely is a formula used for the bonus calculation. The amount of the bonus would not change from the date she left the position to the date you actually received the bonus check. Perhaps the bonus amount was not yet calculated when you moved, but it could have been.
Had you moved to California, for example, the bonus would be both New York AND California income, (although you would get a credit for taxes paid to another state, so you would not be taxed twice on the same income). In your case, you only report it for New York State and New York City.
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