Have stayed at both and think both are great.
That being said, Bonnet Creek is brand new...still building there. The location cannot be beat if you are doing the parks...it is "onsite" ...but not technically since it is not owned by Disney. It is next door to the Caribbean Beach Resort.
The villas were great and are set up similar to the 2 bedroom at the Marriott. Basically the bedrooms are split on either side with the living area/dining area in the middle.
Bonnet Creek has a nice lazy river which I think your kids would love. (Mine do..and so do I).
If you are looking to golf, however, I'd go with the Marriott since it is on a beautiful golf course. For now the Marriott is a larger resort that is more spread out. It is also beautiful and I'd go back there in a heartbeat too.
But for the same price, I'd go with Bonnet Creek for the location, beautiful villas, lazy river.
Have a wonderful time!!!
HeatherC