I need to arrive at HKIA for a 0945 flight on Sunday. How can I reach the airport from Shenzhen?

Hi, you can take the first ferry (departing at 07:45) from Shekou port to HKIA on condition that you need to check in at Shekou Port in advance. As I know, not all the airlines can check in at the port, so you'd better check detailed information. This website may help:
http://www.szgky.com/en/index.asp

Though, time is still very tight. I suggest you go to HKIA one day ahead an stay nearby for overnight to catch your flight in the next morning.