If you tell the independent operators which cruise ship you are on, they will get you back to the ship on time. I have never heard of an independent operator in Alaska not getting their guests back to the ship in time. In fact, many have "guarantees" to get you back to the ship in time or they will pay for your food, lodging and costs to get you to the next port. Then they usually say that in their X decades of doing business, they have never had to use the "guarantee."
I would aim to be back to the ship between 8.30-9pm since all board is usually 1/2 hour before sailaway.