Over half my wages for 2009 were for a large severance package I accepted. I'm assuming I have to pay NY taxes on all of that even though I left NYC and the state immediately upon acceptance. I was only a resident for 4.5 months.

Yes, you WILL have to pay taxes to both NYC and NY state on the severance.

Both governments will take the position that you were resident in the city and state when you received the severance income.