New Chitose Airport: Take the JR Airport Rapid when it runs through to Otaru: roughly 70 minutes, about ¥1,800–2,000, no change. If the next rapid terminates at Sapporo, change there for a Hakodate Line train. The direct airport bus is useful only if your hotel is near its stop or you have heavy luggage: about 90 minutes, so it is not the faster choice.
Sapporo Station: Use the JR Hakodate Line westbound to Otaru. Airport Rapid services do it in about 30 minutes; local trains take longer. Services are frequent—about every 20 minutes through the day—and the fare is roughly ¥800. This is the sensible link; a car or tour bus gains little once traffic and parking are counted.
Otaru Station: This is the correct station for the canal and old financial district: the canal is about a 10-minute walk downhill. For Sakaimachi/Music Box Museum, walk 20–30 minutes along the waterfront and historic streets, or take a local bus/taxi if luggage or ice makes the hill a nuisance. Minami-Otaru is closer to Sakaimachi, but less convenient for first-time orientation.
Otaru Ferry Terminal: For overnight Shin-Nihonkai Ferry arrivals from Niigata or Maizuru, connect onward by local bus or taxi to Otaru Station/the canal area rather than expecting the terminal to be walkable to the sights. Ferries are a transport choice, not a quick arrival: Niigata–Otaru is about 18 hours and Maizuru–Otaru about 20 hours.