@douglasjia suggest you seek another local accountant who can review your tax return. You may be misunderstanding what the current accountant is stating.
While ALL income is reported on the NYS tax return, it is reconciled to display ALL the income versus just the NY earned income. So not sure if you are misunderstanding what your tax pro is stating or he is fraudulently reporting your tax return,
From your example, the tax on $100,000 of income should have been paid to NY and tax on $200,000 of income should have been paid to CA. You lived and worked in CA when you (or your spouse) earned that $200,000 and the tax is due to CA.
It could be conservative to pay everything to NY, because on the whole, the tax rate may be lower and it would save you on state income tax, but it would not be a legal way to do it.
here is the form. Look at LINE 1 - it displays BOTH the TOTAL federal income and the NY STATE income. But when you get to Line 45 it divides the NYS income by the federal income to determine the tax to be paid to NY. The percentage on line 45 should be around 33%. If so, then you only paid tax on the $100,000 of income. if the percentage is around 100%, then something is definately incorrect. Suggest looking at your tax return.
https://www.tax.ny.gov/pdf/current_forms/it/it203_fill_in.pdf
