You need to look at the number of times a day your son has something sugary to eat or drink . Even if it's just a sip or a nibble of something.
In general it's not what they eat or drink at meal times that's the problem , it's what they snack or sip on in between times. Also if they have something to eat or drink just before bedtime, even if you brush teeth afterwards.
This is because every time you have even a tiny bit of sugar the acid produced sits on the teeth for an hour afterwards, longer if you go to bed because the saliva decreases and doesn't wash away and neutralise the acid.
You need to look at things like yogurt, smoothies,raisins , biscuits , fruit juice , flapjacks, grain bars , which contain as much sugar as sweets and fizzy pop. In general if your child has something sweet to eat or drink more than three to four times a day , no matter how many times you brush their teeth , they will get decay.
You need to make the diet changes now , otherwise his adult teeth will decay the same.
Tap water , especially if it is fluoridated is fine and bottled or filtered water is no better for their teeth. However you must also make sure the toothpaste you use contains fluoride as well. It's important that only sugar free drinks are consumed between meals because constantly sipping on drinks or grazing on snacks is the major reason for tooth decay.