In my experience I have sometimes found significant savings booking direct. It is necessary to have all your plans and reservations made in advance. But another consideration with independent touring is you are not with the same cruise passengers on what I feel are quite "insulated tours". Going on your own will give you a feel of some real Alaska. Some of the tours which may be about the same price will also be much better direct - this is especially true with the Juneau whale watching tours. The ship tours will have 150 passengers vs 20 or fewer on an independent with about 30 more minutes sailing- similar price though - at $100+. I never take any ship tours and haven't for the last several years.