First of all, Bonnie Dahl's book " Superior Way" is a great resource. Anchorages at Stockton Island are roomy but all so popular, so both Presque Isle Bay and Julian Bay can get crowded on the weekends. There are other good places to anchor as well, but as Bonnie points out, you need to be aware of the wind direction and how much protection that each anchorage provides or you could be in for a rough night.
Going ashore at Stockton, if you like hiking, has some nice trails. With three days, you would have time to get to Devils Island which has a lot of fascinating sea caves. Others hopefully will share their favorite places.
Although you will generally have plenty of water under your keel, the south end of several islands have a sand spit which extend out a long way from land, so watch your charts and your depth.
I will be up sailing in the Apostles Aug 10-14. Maybe see you there. My boat is in Port Superior Marina.
Hope you have a great time.