My information on North Manitou is dated. I backpacked there years ago (when a young fellow) immediately after the NPS took possession from The Angell Foundation. Often, I would disappear into the "wilds" for weeks at a time.
It used to be very much wilderness camping there. Never any crowds, even on Memorial Day holiday.
My favorite hiking/camping was done on the West side in the woods adjacent to the beaches, and the Southern region of the island. Lake Manitou was also nice, but could at times have mosquitoes.
At the time I was traveling there, raccoons were an issue, and would raid camp for food not well protected. I ALWAYS hung my food (think "bear bagging") at night to lessen the chance of nocturnal visitors.
I have some great memories of North Manitou, and hope the enjoyment I once had can be experienced by future generations.
One further comment: NMI is wilderness backpacking. Be self contained and self sufficient. If you run into trouble you will very likely be dependent upon your own skills and resources. Also, be prepared for an extended stay on the island in case bad weather prevents the ferry from arriving when you have scheduled departure.
--- I never encountered Black Flies, although Mosquito's could be a bother, at times. Good bug repellent, and a choice of campsite where there was a breeze to keep bugs at bay was my tendency.
ETA: NMI takes some time to enjoy. Plan a week at minimum to explore the island. Longer, if possible. Wilderness backpacking/camping is a unique experience.