I'm not really sure how necessary it is to stop the three-month-old from attempting to nurse. Obviously there are potential problems, though I'm not sure how concerning these problems are, such as:
- The kitten isn't getting enough food
- Mother gets injured due to an older cat attempting to nurse
- The three-month-old isn't getting an appropriate diet either due to it filling up on milk
Considering all these potential problems, I would err on the safe side and try to prevent nursing, but you might also consult a vet to get a more definite opinion. It may be that it's not actually a big concern, and you can wait until both are weaned before attempting intervention.
But if you do decide to intervene before the younger kitten is weaned, I think the simplest solution would be to keep the three month old separated while the kitten is still nursing. I've seen a bit of variation in advice on when kittens should be fully weaned, but the longest time I've seen quoted is ten weeks, and most seem to agree that the kitten is old enough it should already be starting the weaning process. In other words, I don't expect that you should have to keep the three-month-old separated for more than a few weeks.
Once the kitten is fully weaned, if the three-month-old still attempts to nurse, there are various things you can do to make nursing impossible, such as covering the mother's stomach with a bandage or even just a sock with the foot cut off if the mother is small enough. Eventually the three-month-old should give up on the idea, and you can stop covering the mother's belly.