Is there still HK airport express @ 1 am going to the city ?

Looks like you'll just miss the last train. This is from the airport website

http://www.hongkongairport.com/eng/transport/to-from-airport/airport-express.html

"The Airport Express takes passengers to Central in just 24 minutes. Quick and comfortable, trains depart at about 10-minute intervals from 05:54 to 23:28 and approximately 12-minute intervals from 23:28 to 00:48 daily."

If you don't want to take a taxi your only alternative is the 'N' route overnight bus from the airport - see

http://www.nwstbus.com.hk/routes/airport-bus/route/index.aspx?intLangID=1

for more information. Which ferry terminal do you want to go to?

N11 Central (Macao Ferry) 00:50 - 04:50 HK$31 via Citybus
N21 Tsim Sha Tsui (Star Ferry) 00:20 - 04:40, HK$23 via Citybus

Thanks! Is it a direct drop off at the terminal?

Sorry, I don't know. But you should be able to find out from Airport Information or if you're lucky the bus driver may speak English.