Go for it!
The archipelago shields you from most of the big waves off Lake Superior, unless you choose to sail exposed to the lake. The Islands are red sandstone, so most have great, pink beaches with good sand for anchoring, and an easy pull to beach a boat.
If you are anchoring, you go for the downwind side of most islands, and be ready to move if the winds shift. The exception is the southeast corner of Stockton Island, where two bays offer protection from all but a rare southeast wind.
If you are going to pull the boat ashore like the many kayakers in the area, then be sure to use one of the campsites, and put all your food in the steel box provided, since the healthy population of bears in the Islands will get it if you don't. Check with the National Shore/Park folks who administer the islands about registering for a campsite.
These are mostly sheltered waters, so if you are confident sailing your boat on a large lake, you will be fine in the Apostles.