As moondog mentions, the departure time of your flight out of HKG is an important determinant whether or not the ferry operator will even sell you a ticket. The confusing thing about the cutoff time is that it varies by airline/destination. I just used the Shekou ferry for the first time last month, and the CX staff told me that U.S.-bound pax need to arrive HKIA at least 120 minutes before scheduled departure. They regularly deny passengers who were unaware of the connecting time, because with the ferry, you are basically transiting Hong Kong instead of entering it. So it's the ferry operator's responsibility, not the airline, to deliver you to HKIA without risking a misconnect and leaving you stuck there with a possible bureaucratic mess.
JL says you need to take a ferry that arrives HKIA at least 110 minutes before your scheduled flight (
link).
For SQ, it's 65 minutes with only hand luggage, 80 minutes with checked luggage (
link).
CX's website has a general statement of 110 minutes, which might or might not contradict what I was told last month, because it referred specifically to U.S. pax (
link).