The New York calculation throws many people off. They do include your total income as taxable, then calculate the tax and reduce it by the percentage of income allocated to other states.
Using your example, let's assume the tax on $100,000 is $10,000. Your New York return will show taxable income of $100,000, then calculate $10,000 in tax. The following step will be to reduce that by 50% (the percentage of income earned out of state), leaving you with $5,000 in tax owed to New York. Using this method allows the state to collect a higher rate of tax on your income, which is why you are not seeing the refund you expect. You can see the calculation on Lines 45 - 47 of your IT-203
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