Hi Tamra!
They are both really great resorts! If the additional money isn't an issue, I definitely recommend the Polynesian. One of the reasons is exactly what you said. Being on the monorail line is a HUGE amenity of the Polynesian. I have an almost 4 and 1 year old and we chose this resort mainly to be so close to the Magic Kingdom. It's just so easy to hop aboard and ride pretty much to your front door.
While Port Orleans French Quarter is lovely and has a beautiful charm, the tropical paradise of the Polynesian can't even be compared. If your boys are water babies, they will love the Polynesian pool. The slide through the volcano is so much fun! PLUS you can watch
Wishes Nighttime Spectacular from right there on the beach!
I also love having a balcony in my room. It gives the room a more "deluxe" feel to it and even makes it seem larger. Having two little ones myself, it's nice to give them more space and my son LOVES hanging out on the balcony and people watching.
I think your kids will LOVE the theme of the Polynesian. My son called it a jungle when we were there last dining at
'Ohana. He pretends to be an explorer and hunts down all the birds, fish, and whatever else he can find. I think as parents, you will really enjoy staying in a deluxe resort as well.
Have a magical day!
Leslie