I am doing a week long trek in Daizetsu San area, but after that am wondering where to go. Should i head back to Sapporo to recover or go to Shiretoko or somewhere else? Ideas appreciated.

Depending on how much time and energy you have you could go on to Shiretoko, I really liked it. Maybe recharge your batteries by resting at a campground for a day or two. The campground around Shiretoko (the one mentioned in the lonely planet hiking book) wasn't much but there were a couple onsens next door.

I'd also recommend Rishiri and/or Rebun islands. Personally I liked the Rebun island hike a bit better because it had some varied scenery.

Shiretoko is a good option if you've got the stamina.

i was completely spent after doing the traverse, and my knees took a nasty beating on all those wooden steps leading down to Tokachi hot spring.

i had trouble walking for a few days afterwards, so if you feel the same as I did, then I recommend chilling out a few days in Biei or Furano - stunningly beautiful countryside with the quilt-like patterns of flowers that Hokkaido is famous for.