Basically you will need to pre-book a private charter for your group which can leave anytime you wish for 29,000yen for 1-2 people, 35,000yen for up to 5 people and 45,000yen for up to 9 people one way.
If you'd rather not take the private transfer we suggest spending a night in Chitose or Sapporo city then coming to Niseko in the morning. If you want to get to Niseko as early as possible staying at Sapporo would be the go as trains depart from Sapporo for Niseko as early as 06:51 getting to Niseko (Kutchan station) at 07:50. From Chitose airport it takes 40 minutes to get to Sapporo station.
If you stay at Chitose the only direct transfer option to Niseko is the bus, the earliest bus departs for Niseko at 9:30 arriving at 12:00. If you choose to stay in Sapporo then we suggest staying near Sapporo station. If you choose to stay in Chitose then stay near the airport or Chitose train station in Chitose city, a ten minute train/taxi ride from the airport.