I worked in NYC all last year of 2007. But I moved from NYC to NJ end of February 2007.
The wrinkle is that I got paid a bonus in Jan and paid NYC city taxes on the bonus.
Since I moved to NJ in February, can I prorate the bonus over the year and get a refund on the city taxes I paid?
Thanks!

Nope - sorry. You received the money in January, so NYC gets its share of it.

You may be thinking that since your W-2 reports your total pay for the year, and if you pro-rated your total 2007 salary it would seem unlikely that NYC would be any the wiser. I would be concerned that they may in fact be smart enough to see from your records that you had a spike in your withholding in January, which could cause them to investigate further. Personally I would pay what's owed NYC and not take the risk of being charged for tax fraud.