Hello and welcome!
I always recommend folks book directly with the vendors in AK. 99 out of 100 tours will be available directly, for the same tour. Often, you'll save the 20-30%++ commissions the ships charge. Even if there's not a monetary savings, you'll certainly get more tour time, or at the very least more "value" for your dollar with smaller crowds, special lunches/gifts, etc.
I know of one excursion here in Juneau that's the same price on the ship vs. direct with the contractor, but the ship's tour is 4 hours long and the same tour booked direct is 5 hours. For a fishing excursion especially, more time on the water is always a good thing!
The ONE EXCEPTION to my advice above is if you know specifically which vendor will be fulfilling your ship-booked tour, and you want to go with them specifically, but there aren't any direct seats available. The WP&YR in Skagway and the 5-hour salmon fishing / whale watching combo in Juneau... There's only one train company in Skagway, and only one fancy 6-pack charter boat that's running combo trips in Juneau. If you're going the direct route for a ship's tour, however, don't tell the vendor that you're on a cruise. Just check availability for the day/time/tour you want, and be done with it. Many of us who contract with the cruise lines have agreed to ask clients to book on the ship if we know that's an option.
I haven't had my coffee yet today, so I hope I've explained that well enough to be intelligible...
Happy Alaska Travels!
Better not for now... signatures get me banned!