Mapple produces a series of maps covering the major mountains in Japan.  They have 60 maps; three of which cover Hokkaido.

No. 1 covers Rishiri, Rebun, Shari and Akan

No. 2 covers the Niseko area (Yotei).

No. 3 covers Taisetsu and the Obihiro area.

The guides look like this and can be purchased in most book stores as well as online.  They include all the trails, trail times and topographical information.  I always copy the section I'm planning to hike, put it in a waterproof map case (aka big ziplock) and take that along.  That way, I never ruin the original and don't have to attempt to fold up a large map in the wind or rain.

They cost 800 Yen each plus tax.