I don't think you can go wrong with either. We have stayed at both - our son will be 5 this month - and have another trip planned for winter. Each of our stays has included nights at the Polynesian. I was surprised that, at least so far, the volcano pool has somehow held more interest for our son than the monorail going through the CR (I would have guessed the opposite). He did very much enjoy seeing the castle and fireworks from our room at CR, but still preferred Polynesian. For us as parents, it is sort of a toss up. I would not personally bother paying for MK view at the Polynesian since it seems so much farther away, and we have had really lovely views from GV rooms there. I prefer the MK view at night from CR, when the parking lot isn't as prominent. Some folks don't mind seeing the lot. Walking to MK from CR is a great perk, and walking to either the "regular" monorail or Epcot monorail from Polynesian is great. We have also taken advantage of buses from TTC to AK and DHS while staying at the Poly. Not sure if it is really quicker, or just seems that way. On our next trip we are once again staying at the Polynesian (split with S/D), but I would never rule out CR. We could always still end up switching since it won't necessarily be warm enough for the volcano pool, which is the main draw for our son. I do agree with the PP that the volcano pool can get annoyingly crowded at peak times, by the way, although our son doesn't seem to notice.
Good luck with your choice!