A few years back we (myself and husband), did a very similar trip. In Prince George we stayed at the DaysInn IIRC. It was good in that it was a level walk of maybe 5-10 minutes from the station, quite doable trundling overnight luggage. At that time anyway, the VIA train crew assured us it was OK to leave our main luggage on the train. This was a medium type place, quite reasonable. We were glad of its proximity to the station, as there were few taxis and there was a long wait for those who needed them. The few taxis went backwards and forwards delivering passengers to more distant destinations, but I would have been anxious in the morning if we had to depend on scarce taxis to get us back to the station.
Can't remember where we stayed in Prince Rupert, but I can check on that. There is a great Indian museum there, well worth a visit.
We were a little disappointed in Lake Louise, in that it was very "touristy". I know that we were tourists too, but we like places that are less crowded and developed. I wouldn't dream of paying such a huge amount. Presuming you will have a hire car, Banff is close by and there should be much more reasonable places to stay and you can drive a bit to see views just as good in more relaxed conditions. I felt the lovely lake was spoiled by the multi-storey hotel buildings.