We have taken both routes at one time or another. We have booked local tours in Ketchikan and rented a car in Juneau with no trouble at all. We have also taken some wonderful cruise line shore excursions that have been worth every penny. One excursion we have taken several times is a photo tour in Juneau that has both a land and water portion to it and is led by a local photographer/guide. Activities that are weather dependent such as taking the tram to the top of Mount Roberts in Juneau should be booked when you get to shore. The cost is essentially the same as booking through the cruise line but you might want to see if the mountain is shrouded in rain or mist before going up.
Something you will need to consider is the ship will only wait for late tours if they have been booked through the cruise line. If you are on your own, plan on returning LONG before the ship requires you to be back on board (times are always posted in your cabin newspaper the night before and on the gangway). Don't miss the ship - it really won't wait for you if you are on your own. We have seen passengers left behind on the dock, trying to charter a fishing skiff to ferry them out to the departing ship!