Both are great, so here are some of the comparisons:
Poly: Themed to the South Pacific islands. Rooms more rustic, tans, browns, etc. Nicely themed pools. No hot tubs, Relaxing, laid back atmosphere. On monorail line, and within walking distance of the TTC. Nice restaurants, and a great lounge. Nice beach with swings, hammocks, chairs. Nice view of MK from beach. Boat to MK. Boat rentals. Great CM's.
Contemporary: not really themed, but lots of Mickey there. Home of Chef Mickey's and California Grille, bright and energetic, large rooms, slightly larger than the Poly, rooms very brightly decorated, balconies on Tower rooms only, patios on 1st floor wing rooms, best bathroom layout in all of the Disney resorts. Recently renovated, 2 nice large pools, one with slide. Hot tubs, kids playground, boat rental, boat to MK, WL and Fort Wilderness. Walking distance to MK. On monorail line, in fact it goes through the building. Sandy beach overlooking Bay Lake. Great CM's!
It really is a matter of personal taste. Personally, I would be happy at either. Good luck on your decision!