Every year I fly into Houghton with my limited backpacking equipment. I say limited because in past years I have been going as a volunteer with the IRNHA service trip and so I only had to bring a tent and sleeping bag, not food or cooking supplies. I did not trust my backpack to go bare on the commercial airline, though some people do it. I was just too worried about all those straps getting caught somewhere in the luggage handling system. I had a large suitcase that the backpack would fit in, so I flew it empty inside the suitcase and packed the contents in a rolling duffle along with my "civilian" clothes for before and after. I would then have two checked bags, neither of which was overweight. Although now you would pay out the nose for the two bags, when I flew last year they still only charged a fee for the second. So I have not tried shipping bags to Houghton ahead of time. I'm not sure who would receive them for you there. However, I do know that they store extra luggage for people who are taking the sea plane to the island. You need to contact Dennis, the airport manager, ahead of time. Basically they are just locking your luggage in an office while you are gone. The caveat is that you can only pick it up when the office personnel are there during daytime business hours, but if you come in on the seaplane that shouldn't be an issue.
As for the seaplane, it is great, and I love it to pieces, but there are things to keep in mind. He can only carry so much weight and he's not going to make any exceptions. Since you are already under constraints by the commercial airline, you should not have a problem there.
Also: the pilot only has the schedule for the day with him, so you can't double check with him on what time you agreed to be picked up to go home when you're on the way over to the island. It's too late to ask then because he has no way of knowing. That's all on you, so don't get confused (like I did!

.) You MUST be at the dock about 30 minutes before you are supposed to fly out. An hour early is better. There are worse places to kill an hour than Tobin Harbor, so that's not bad. If he gets a chance to arrive early, he will, and if you're there, he'll go ahead and go. If he's late, he's late. If you want to catch a flight out of Houghton the same day you take the sea plane back, schedule your return as many hours ahead of time as you can stand. Remember, once you are on IR you are on island time and human schedules count for nothing. Less than nothing. Weather rules. If you aren't at the dock he might make a cursory search for you in the immediate vicinity, but that's not a given. If you're not there he'll go without you and if that means you miss your flight out of Houghton, he can't help it. Rebooking fees are steep so don't be like me and forget what time you said you wanted to leave! (It was not the pilot's fault at all; I had the absolutely wrong time fixed in my mind and hadn't been smart enough to bring a copy of the receipt as a reminder.) Frankly, I wouldn't try to go home the same day again. Besides the chance of missing the connection, it's too much of a culture shock for one day. Houghton is a good place to ease back into civilization. It takes a while to start remembering to flush again

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I usually stay at the Best Western in downtown Houghton before and/or after a trip to the island because it runs an airport shuttle and you don't need a car. Their rooms are very comfy. Also, if you stay at the BW on your way in or out of town, they will store your luggage for you for free while you are on the island.
I'm curious... have you been able to book a flight to Houghton for this summer? Mesaba is no longer the regional carrier, now it is Skywest, and the last time I checked, they weren't accepting reservations for the summer yet. The Daily Mining Gazette had an article that suggested the fares may be quite high, and daily flights have been cut from three a day to only two. I haven't seen the times yet. Kind of dreading it.