Hi Sean, and welcome to cruise-chat.com.
If you want to book with the cruise line, make a beeline for the shore excursion desk the moment it opens.
As you mention, booking with the vendor may be an option, and one that several of our Members have done. You can scroll down the list of posts on our Alaska board to learn of their experiences... and I'm sure that some will respond to this thread, also.
But, if you want to book through the ship, act quickly once onboard.