Budget
Minshuku Oyado TenshÅ
Cheap Minshuku by the port, if the two hostels are not your thing. A 15 minute walk from the ferry terminal. Clean rooms and wireless internet.
Moshiripa Youth Hostel
Tricky to find, but a good hostel. Large common area with a big TV, games and books. Friendly managers, one of them speaks English surprisingly well, though not fluent by any means. The shower times can be a bit annoying, and it can get a bit cold at times.
Midrange
Dormy Inn
Fairly large business hotel, which has a nice spa on the top floor, both indoors and outdoors with views over Wakkanai, which are free for guests. Small rooms, but no smaller than usual in Japan, and a great breakfast buffet.
Hotel Joy
Central no frills business style hotel, small basic rooms with even smaller windows, but the singles are OK for the price.
Wakkanai Grand Hotel
Definitely not a pretty hotel, but a large section is recently refurbished so it's not so bad on the inside. The hotel's private spa is nice, and they have a large restaurant and bar as well.
Top end
ANA Hotel
The most upscale hotel in town, and also the most expensive. But you pay for the very good facilities and common area's, not the rooms which are fairly standard, although some with nice views over the sea or Wakkanai koen. The main restaurant is very good, and so is the complementary breakfast.
Wakkanai Sun Hotel
Has free wifi in the lobby, however non-smokers be warned: every room is a smoking room.
There are three large hotels in Wakkanai: the ANA hotel, the Wakkanai Sun Hotel and the Dormy Inn. They are all quite pricey, however. Expect ¥8000 for a single room and ¥16,000 for a double. One can wonder why a small town with 40,000 inhabitants needs a great luxury hotel like the ANA hotel. The answer is probably an influx tourists. All directions given below assume you're starting at the main railway station.