My kid is still pre-HS, but I wanted to add a bit more to the academic side of this discussion. There is a lot to be said for having all 4 years at one school. Learning which professors to take and which to not, accruing credits so you can park on campus, not having to deal with certain credits not transferring correctly, as well as the social aspect.
My 4 years in college were probably the most formative years aside from age 1-5. I understand having a passion for baseball, but please consider the child/man in this scenario...baseball ends, it does for even the most talented players, but the next 4 years will shape a great deal of the man that he will one day be. Knowing he would have to leave the JUCO in 1-2 years doesn't make for a nice stable environment where he can explore who he is as a person outside of baseball.
If he was MLB level and just needed to get his grades up my advice might be different, but that isn't what he appears to be. Just consider the future of the boy in this scenario as much as the baseball. It's great to have a dream, but not at the expense of a future life.