Buses (¥300, 15 minutes) run irregularly (and infrequently in summer) between JR Kutchan Station and the ski villages; it's better to arrange pickup.
During snow season, Niseko United Shuttle (www.niseko.ne.jp) runs a service (roughly hourly 8am to 11pm) between Hirafu, Niseko Village and Annupuri (free for all-mountain pass holders). From 5pm to 11pm, the shuttle route extends to JR Kutchan Station, giving you more dining options. Pick up a schedule from any of the tourist information centres.
Niseko suffers from a chronic taxi shortage during the ski season, as most are booked up in advance. Most likely your lodging will offer to shuttle you around (for a fee), which is usually cheaper than taxis and more reliable. If you do need to use a taxi, have your accommodation call ahead for you.