The following places can do check-in for UA HKG-bound flight in HK:

1) HKG Airport
2) MTR Kowloon Station
3) MTR Hong Kong Station
4) Skypier (For pax from Mainland China or Macau, you will get HK airport tax refund as well )

2-3 requires 3 hours advance check-in, 1 and 4 allow check up up to 60 min before the flight.

Note: You need to catch a ferry that is departing 3 hours before departure of your floight in order to use 4

Correct me if I am wrong