My son also plays multiple sports. He is a junior this year. Just this year he dropped basketball from his list of soccer and baseball. He has always played 3 sports. We found that basketball was the least favorite if he had to drop one and he has focused much of his winter season working on increasing his strength and focusing on pitching.
It all depends on which one he sees himself at when it comes time to think about playing at a higher level. I have watched my son grow in both soccer and baseball. Baseball is his passion though. You shouldn't have to decide between sports if he is having fun and enjoying them all. But there will probably come a time where you start to see those kids who focus on one sport year round start to excel a little bit more. At least that was in our case.