Favorite Thing: I get asked a lot on what to do with a day in Juneau so here are some general tips.
If you have an aversion to crowds like me, you might find downtown Juneau to be very touristy and crowded when the ships are in. I had been often during the legislative sessions and downtown was a pleasant and quiet place. But when we went to visit our daughter a few years back during the summer, I was amazed at how those few blocks around the cruise docks was packed with people and all those stores that are usually shuttered close are open and selling every kind of trinket, usually made in China or some expensive jewelry made of black pearls or something else that has nothing to do with Alaska. There are some nice shops mingled in amongst the kitch such as local art.
The Mt. Robert's tram leaves right from the cruise ship docks - you can't miss the bright red cable cars. But it is efficiently run and folks move through fairly quickly. A restaurant up top that serves so-so food but a great view. The bird rehab group had an eagle for close up viewing that was recovering from an injury the time we went.
A walking tour of the rest of downtown can be pleasant. Staright up Franklin Street will take you to the State Capital. A modest 4 storey building built in the early 60's but packed with lots of historical photos and displays. The State Museum is worth a visit - perhaps the nicest in Alaska besides the main one in Anchorage. The Governor's Mansion is right on the sidewalk so you can get very close. Past the Mansion is a nice park (Cope?) that leads back into Propectors Creek with some nice trails in the trees and an old gold mine.
If you rent a car you can drive out north of Juneau. St. Therese's Shrine is a wonderful spot to walk around and about 8 miles north of town. Some nice beaches further north that are rarely crowded.
Best restaurants during the summer are the Twisted Fish and the Hanger, both right down by the cruise ships.
Can't speak to the helicopter rides. But the whale watching boats are usually successful in finding whales and you can save a few bucks by booking online instead of going thru the cruise line. Get away from their vertical integration and keep some money in your pocket.
There is a bus from the docks to Mendenhall Glacier for $7.50 OW. I've seen a lot of glaciers in my time and this is one of the more accessible and scenic. Nice visitors center and there is a trail that takes you close to the actual ice (about 1/2 mile). Easy walk if the water level in the lake is low. Trail ends at the waterfall.
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