If you REALLY want to go on a particular excursion, it's probably better to pre-register.
But a lot of them are ALSO available from private vendors just as you get off the ship -- sometimes a bit cheaper, sometimes for the same price.
And some -- like the whale watching -- are supposed to be better to go to a private vendor (prior to your cruise) and book directly. Most of the private vendors will work around the cruise ship schedules.
Which are you interested in? Maybe if you're more specific about which excursion, folks can be more helpful
(Like, I know the whitehorse train thing can be booked simply as you get off the ship; I went direct to the source for the whale watching....)