Personally, I think in Alaska, booking yourself is easy to do, depending on excursion you are interested in. Several years ago, we had an awesome whale watching tour self-booked in Juneau. We had an easy time renting a car in Skagway.
I'd rather book myself because of smaller tours and cheaper options. But you have to really study to make sure they are reliable, will get you back on time... give you refund if your ship doesn't make the port, etc. So it is a little more hassle.
One of my favorite examples is hiring a taxi/van and seeing sites in Maine... seeing the bus from the ship all lined up waiting for restrooms, etc.... the unloading, loading... marching to someone elses time frame. And us jumping in and out and extra stops and being able to do exactly what we want. Can't always have that opportunity tho.