Both resorts are excellent -- you can't go wrong.
However, For a Disney trip, you can't beat the location of WBC. Harbour Lake can feel a lot farther because of traffic. It just isn't as convenient.
When we went to Harbour Lake a few years ago, they had lots of fun activities for kids all day long. My kids didn't want to leave the resort to go to the parks.
At Bonnet Creek, they also have fun activities, but you feel like you are within Disney, so it was easier to get our crowd moving to the parks.
Anyhow, my advice is that for a Disney trip stick to WBC. Especially a shorter trip, where every minute counts.
If you are planning a longer trip and want to visit Sea World and enjoy some downtime with younger kids, I like Harbour Lake.