Yes, the ferry from Hk airport to Nansha port, Panyu, Guangzhou departs at 11:40 and 15:50 .

I WILL REACH HONG KONG AIR PORT AT 8.00 AM MORNING. WHICH IS THE BEST MODE OF TRANSPORT TO REACH PANYU, GUANGZHOU? - BY FERRY ITS AT 11.40 VERY LATE OR SHOULD I TAKE TRAIN FROM HONG KONG TO GUANGZHOU? OR SHOULD I GO TO SHENZHEN BY FERRY AND THEN TAKE TRAIN FROM SHENZHEN TO GUANGZHOU?
PLEASE GUIDE

Actually, I think it is much easier for you to take a coach from Hong Kong Airport to Panyu, Guangzhou. Upon arrival, you could follow the directions to take the cross-border to Guangzhou on the spot. Both of the bus schedule and fare could be found on the official website of Hong Kong Airport.