Filters or CS5/LR3?
...If you were thinking about a seprate polarising filter, personally I would not bother. This is only of much use in good light. I have been on the Inca Trail in cloudy and wet conditions, and there is not much light around then, and you will lose a lot more light through a polarising filter...
I'd take a polarizing filter. The added weight is really negligible and who knows but that the sun might come out and it might not be cloudy and wet for the whole trip. Surely you will be in other places on the trip where the sun will shine?