I live in NYC and was also confused by the discrepancy. I assume it is different state by state and locality by locality, but for me the math was:
tax refund = total refund - Line 69 - line 69a (NYC school tax credit items)
The 1099-G you can get from the state aligned with what turbotax imported from my previous year's return. Strange that they have a locality option for "New York City, NY", but refund reporting seems to be at the state level.
