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If you arrive in Juneau by plane or by ferry without your car you may want to either rent a car or travel by taxi. The following is a listing of rental car and taxi companies in the Juneau area:
Budget Rent-a-Car: Their Juneau office has a key drop-off box at the Marine Highway Ferry Terminal for easy car return for ferry passengers.
Evergreen Taxi: Reserve a taxi for a tour, to meet you at the airport or ferry, or to get around town. For immediate dispatch, phone (907) 586-2121.
Rent a Wreck: They have a cruise ship location, and a second location. Will make arrangements for ferry terminal pick up, and will drive you to the airport after dropping car off. But careful -- complaints have been made about their treatment of customers.
Note: Rent-a-Wreck apparently is now called Juneau Car Rental Company.
http://www.juneaucarrentals.com/ . They were super friendly and cheaper than other options. Definitely would recommend them for cruise ship passengers, since they're within walking distance of most of the docks.