I've been going over to the Manitou islands for almost 20 years and have not had a bad experience. I'm shocked to read some people were disappointed with the ferry service. They are an experienced third generation sailing family.
First of all leave your backpack at the dock when you go and park your car, then you wont have to carry it back. I've never had mine tampered with.
Crowded. I've only experienced overcrowding on Memorial day or Labor day or other major holidays. They do that so no one is left behind. Most of the time people move around and go up on the upper deck for a while so you can usually find a seat sometime.
Have an uncomfortable trip? Well that's Lake Michigan for you. I personally like the fact that some people find the boat trip unpleasant. It keeps the island from being over run with noisy screaming kids and obnoxious people. The kind of people that go there are people who love and respect the outdoors and love our national and state parks and don't mind a bit of a challenge to experience them.
Its pure heaven over there. Its my favorite place to be in the outdoors and recharge my mental batteries. If you want to be assured there will be absolutely no challenges, rough weather or last minute disrupted schedules due to storms, then stay on the mainland in a state park with your big campers, radios, and generators. I've certainly put up with your kind before and I say "Good Riddance." I'll be sitting on top of the western sand dunes watching the sunset with my son and glass of Crown Royal.