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....)
If the cruise line allows you to book in advance and you have found a tour you want I woul book inadvance because they can fill up. If you decide you do not want to take that tour usually you can change your mind as long as you notify the cruise line 24 hours in advance of the tour. There are many reputable tours from local tour guides that you can find at the pier also or on the internet. The one advantage to a cruise line tour is if the tour for some reason is going to arrive back at the ship late the ship will wait because it knows there was a problem. If you just go with a local guide and say their bus breaks down the ship has no idea where you are and could leave without you.