Tough call. However, it is a not an unusual approach for a school to throw in a "reply by" date. With that said, you do not want to get into the signing period and be left out in the cold with no where to go. On the other hand, you do not want to throw all your eggs in one basket to early. I think I would call the choice #1 and let them know of the circumstance being very careful not to put it in a threatening tone, just informational letting them know that they are #1 on your list and you wanted to let them know of the situation out of respect for the program. If they balk or throw out a non-exceptable offer, maybe you are not so high on their list, if they put out a qualifying offer it may be the time to jump in.
One thing to keep in mind is sometimes the #1 choice is the personal favorite, but not necessarily the best "fit". This is a big decision that can happen in the wink of an eye. Sit down with your son and matrix on paper the pros and cons of each school incluing academics, lifestyle, family issues, costs, and baseball program. You would be surprised how the realities of a situation look on paper versus mulling them over in your head.
After posting my reply I see that Justbaseball and I are on the same page