will u be driving? if so, that will be best - so much more convenient! otherwise, u can go to the ticket booth near the JR Sapporo station/bus terminus and sign up for local tours... (ps: these tours are conducted in japanese - very little english is spoken). check out these websites: http://www.japan-guide.com/ and http://www.jnto.go.jp/ (not sure if any mentioned shakotan.. if have time, should go)
hopefully it's not the peak period - might have problems looking for accomodation if so (japanese normally book at least a mth in advance). try the nakamuraya ryokan in sapporo... excellent food and service (again, very little english spoken)..