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At 6 years old, the real difference comes down more to the approach than the discipline itself. Judo is easier for little kids to understand because it's all contact, rolling, and controlled falls - he'll quickly learn how to be comfortable on the ground and won't be afraid. Taekwondo, on the other hand, requires more coordination and mental discipline, so if your son already has good focus he might do well with it, but some kids that age get a bit bored standing around doing forms.
It also depends on what you want him to develop. If you're looking for confidence and pure fun, judo is perfect because it's more playful. If you want him to work on posture, balance, and learn to kick fast, taekwondo is good. The most important thing is that at 6 years old he goes somewhere with a good instructor who has experience with small children and isn't too strict - motivation is everything.
Try to get him to do a couple of lessons in both if you can, see which one he enjoys more. At that age, enthusiasm matters more than anything.
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