I was wondering what the pros/cons where for booking port trips with either the cruise line or through a direct booking. How much cheaper are the direct bookings? Do they provide transportation from the dock to the site? Any help would be a great help.
The pro to going with the ship is that you are 100% guaranteed that the ship will not leave without you should something go wrong. That being said, if you leave sufficient clearance and discuss how much clearance with the tour operator, you really shouldn't have an issue in this regard. So, fear (often unjustified fear) is the reason to book with the ship.
Going independent sometimes saves you money (particularly if you have a 2-for-1 coupon). But there are nonmonetary benefits to consider as well. Independents usually provide smaller group sizes, which means more interaction with the guide and the ability to tailor the excursion to your likings a bit. Independent also is more likely to give you knowledgable local guides rather than people who are just working there for the summer and know less than the tourists. [Of course, there are definite exceptions ... Gastineau Guiding does hikes in Juneau that are ship booked and Northstar Trekking does as well, both are exceptional in terms of these issues.] Sometimes going independent actually costs more, but these quality issues make it a far better deal. For instance, we went kayaking in Ketchikan with S.E. Sea Kayaks for more than booking the ship's kayak tour and ended up on a private tour with just the 2 of us and the guide (max would have been 6 people) for great secluded wilderness experience and then had an amazing snack/meal they provided. These boards will help you find the right independent operator for you if you give us your interests.
Whether transportation is provided depends on the provider. Often they meet you at the dock and walk you to where you need to be or they have operations so close that they can easily tell you how to walk to their operations. Other times, you will be expected to provide your own transportation.
I never book ship tours, the independents may not be cheaper but they are always better with less people and more personal attention. A lot of ship tours are staffed with seasonal guides. I have taken over 100 Alaska tours, if you miss your ship- it's your own fault for poor planning. I recommend if you go the independent route- always fully disclose your ship and port times, and always go with the vender's recommendation. You never see any posts blaming Alaska venders for missed ships- because it doesn't happen. Most always transportation is provided from the ship.