Welcome Mallard -

June has historically been labeled "bug month" in canoe country and on a typical year all varieties of winged critters are at their peak.  That said, however, the title of your thread is appropriate ... its all about timing.  I've been on canoe trips in June where the bug population (even skeets) were minimal ... but I typically plan for them to be bad (e.g. treated clothing, head nets, plenty of deet, etc.)

Another issue not mentioned is your interest in fishing.  Assuming that might be an important point (since you are base camping), I suspect you might want to be on the water and ready to fish on the Saturday, 2 weeks prior to memorial day (historic opening day for Walleye in Minnesota).  So, a mid-to late-May might be your choice.  Certainly less bugs then, and fishing usually among the best of the year (all species will be relatively shallow that time of year).  The down side is you have to be prepared for some foul/cold weather.

dd