WL
Pros - price compared to Poly, beautiful resort, boat to MK, all rooms in main building, bigger variety of food/snacks sold at shop, Whispering Canyon
Cons - pool, we experienced long line for boat at MK close,
Poly-
Pros - the pool (zero-entry), monorail, character breakfast, easy walk to Epcot monorail, awesome view of Wishes, theme, larger rooms, 'Ohanas is fun and great food!
Cons - only one I can really think of is $$ more than WL
With young children we greatly prefer the monorail resorts for convenience to the MK, you just can't beat the monorail. If cost is a big factor I would choose the WL. You really cannot go wrong either way. If you choose WL I would go with deluxe room for the extra space.