Another question to ask yourself would be is where you see you and your family in 5 or 10 years.. Good luck with your decision! Let me know if I can be of further assistance!
Both communities would be a wonderful place to live and raise a family. Both developments have easy access to shopping, transportation, great schools, and much more. If I were assisting you in your purchase, I would suggest that you get a feel for the surrounding areas of these two developments and cities. I am very familiar with both communities and recognize that they both have very different characteristics.
I think it is hard for anyone to give you a specific answer as to which is better... this is YOUR house not ours so you have to look at them and consider which is right for you. Both are great communities with schools with great reputations so it boils down to what's most important to you. All things being nearly equal, price may be more important to you versus location for someone else.
It's a tough decision to make, but I believe it is a decision best made yourself.
By the way, Apple Valley schools continually rank high in the state and it is pretty easy to get around. They are also in the process of finishing a huge sports complex (baseball) just west of Cobblestone Lake, not too mention the future connection of Cobblestone with Brandjten Farms via walking paths etc. One pro I like about living south of the river, instead of in Woodbury, is the proximity to I-35, and ease of getting to either Saint Paul, Minneapolis. Hope this helps!