Under Settings > General > iTunes Wi-Fi Sync, you can click a button to make it sync when it's not connected. I think this is a one time only button, you have to click it every time you want to sync.
My iTunes will see my iPhone when my iPhone is not plugged in, and it will sync. I read somewhere that the iCloud sync will take place if your battery is over 50%. Perhaps the iTunes sync is really like that also.