For two young boys, go with the Contemporary. I love the Poly, and would prefer to stay there myself. But your boys will love the monorail going through the hotel. When I was seven and stayed there I loved it, and could watch the monorail all day long. Get a tower room and they can sit outside the door to the room and watch the monorail.
The CR also has a great 24 hour food court, a huge arcade, and Chef Mickey's (a favorite restaurant for a character meal). It's a short walk to MK (and the first monorail stop on the way back). Getting to Epcot is fairly easy: one stop to TTC and switch to the Epcot monorail (returning is a little harder because CR is the last stop on the resort loop from the TTC).
The poly is good but I think a lot of the tropical theming is lost on young kids. The food court is very small and basic and the arcade is just okay. The volcano pool at Poly is probably better than CR and they do have 'Ohana's, another great restaurant for character meals.
You won't go wrong with any monorail resort. But, with the monorail going through the resort and its proximity to MK, CR is the best choice for two young boys, IMHO.