The last domestic flight from Narita (NRT)to Sapporo Chitose is 19:00.
The last flight from Haneda (HND) airport to Sapporo Chitose (CTS) is 23:30 which lands after the last train to Sapporo (22:50) and the last bus to the Niseko Resort Area at 21:30.  Arriving in Chitose after the last train and bus, your options are limited to staying in Chitose or a private shuttle to Niseko which needs to be arranged in advance.
The best option would be to spend a night in Tokyo near Haneda (HND) airport and catch a morning flight to Sapporo Chitose (CTS).

The two major Japanese airlines ANA and JAL operate domestic flights daily from Kansai International Airport (KIX). Budget airlines Jetstar and PEACH also operate daily from Kansai.  Please note that Osaka has another airport that is also used for domestic flights called Itami Airport (ITM). 

The Chitose-Tokyo route is the busiest domestic air route in Japan and one of the world’s busiest handling over 8 million passengers annually. The two major Japanese airlines ANA and JAL plus discount carriers Skymark, and AirDO operate on this route.

There are direct shuttle buses that link Narita and Haneda airports. The cost is 3,000yen and the journey takes approximately 75 minutes depending on traffic. No need for prior reservations. More information can be found here: www.limousinebus.co.jp

Several airlines operate daily from Narita to Chitose-Sapporo. These include budget airlines Jetstar, AirAsia and Skymark. National carriers ANA and JAL also have daily flights. It is also possible to fly from Tokyo Haneda Airport (HND) but this will require a 90 minute transfer via bus from Narita. 

Most people arrive in Japan via one of the two main international airports, Tokyo Narita (NRT) or Osaka Kansai (KIX). Most major airlines such as Qantas, Singapore Airlines, JAL and budget carriers such as Jetstar have regular flights to Tokyo and Osaka.

• All Nippon Airways (excludes Australia and New Zealand)

• Cathay Pacific Airways

• Continental Micronesia

• EVA Air (Taiwan)

• Japan Airlines

• Korean Air

• Air China
• China Eastern Airlines
• JIn Air (Korea)

The closest international airport to the Niseko Resort Area is New Chitose International Airport (CTS) also referred to as Sapporo Chitose (CTS). The airport is located in Chitose city which is 36km south east of Sapporo city and 115km east of the Niseko Resort Area. Information for New Chitose airport can be found here Chitose airport