I cannot recommend the Lighthouse & Marine Wildlife tour. Ours was 4 hours of riding around in an enclosed boat with very few minutes allowed on the observation platform. We had 5-7 foot seas at one point and it was not fun in that 30 passenger boat. We finally saw a humpback whale for a little while - mostly blowing and just skimming the water for more air and then gone.
For perspective, my flight home today is only an hour or so longer than that boat ride was. We heard the grizzly bear tour was better and they saw lots of stuff.
The town is neat, clean, and easy to access. Be aware that some of the citizens would prefer that cruise ships didn't stop in Prince Rupert. These people are also opposed to the large container ship port that has been built. It isn't a pervasive opinion though. Most locals are very friendly and helpful.