Is it better to use MTR or bus from Hong Kong Airport to Ngong Ping 360?

Taking a bus + cable car may be a better way.
You can take bus line S1 from Car Park 1, Cheong Tat Road Station to Tung Chung Railway Station Bus Terminus. The trip takes about 25 minutes, and the fare is HKD 3.5. Then walk to the cable car lower terminus and take it. :)