There’s no cheap way to get kayaks into Gustavus.
The ferry option is unattractive, because you’d have to drive to Prince Rupert, stash your car in town, ferry to Juneau, and then ferry to Gustavus. The ferry to Gustavus isn’t coordinated with the ferry to Juneau, so you will likely lose several days in Juneau waiting for your ferry to Gustavus. And then you will lose several more days in Juneau on the way home, waiting for your ferry back to Prince Rupert. These wasted layover days will come in addition to the days you will already lose during the actual sailings themselves.
Consider, too, the expense and inconvenience of layover days in Juneau. Where will you stay, what will you eat? The nearest campground in Juneau is miles from the ferry terminal. There are motels within walking distance of the ferry terminal, but they’re expensive, and what will you do with your kayaks?
You can avoid layover days in Juneau by chartering a water taxi between Juneau and Gustavus, although caution: the ferry terminal is nowhere near the water taxi marina. With four people splitting the cost, a water taxi might not be too much more expensive than the ferry would have been, but it won’t be cheap, especially if you use a water taxi both ways. Of course, the ferry itself isn’t all that cheap, as you have no doubt discovered already!
Gustavus isn’t at all a walkable town, even with kayak carts. Once you arrive by ferry or water taxi you will still have to car-taxi your four kayaks and gear around. Depending what time of day you arrive, you may have to car-taxi to a hotel and spend the night before you can car-taxi to the national park headquarters at Bartlett Cove for mandatory orientation the next morning. There are only one or two car-taxis in Gustavus, so you’ll need to reserve these movements ahead of time, or else you may be stranded at the ferry terminal or at your hotel for half a day.
You could bring your own car with you on the ferry, but this would massively increase your ferry costs and also preclude you from using water taxis, thereby committing you to losing the maximum number of days lost to layovers and sailings. Also, I would be surprised if the National Park Service would let you leave your car in Bartlett Cove during your trip, so you’d probably still need at least one car-taxi even if you did bring your own car.
Instead of all that nonsense, your best bet is probably to fly into Gustavus and rent kayaks. Your outfitter will meet you at the airport with everything you need and all transportation arranged.
The only way it makes sense to haul your own kayaks into town is if you will be out for a very long time, like four weeks or more. At that point, the kayak rental fees climb so high it starts to make sense to haul in your own boats ... assuming you can afford to squander some of your vacation days dealing with ferries and water taxis.
Alex
One final tip, which I learned the hard way. It’s pronounced Gus-TAY-vus, not GUS-tuh-vus.