Some of the questions are standard ones you've probably already thought of. Why do you want me in particular and where do you see me fitting in on this team? Here I would be blunt and ask for an honest assessment by the coach. Really listen to the actual answer, as so many folks hear what they want to hear rather than what the coach actually says. E.g, "you have a chance to play this year," is often interpreted as "I'll be the star of the team starting almost every game, if not every game." When in actuality it usually means, "you have the same chance of starting this year as you do of finding the cure for cancer." Haha.
Ask if coach sees you starting by year two or three and in what capacity. Look for certain answers, and take note of vague ones. Coaches who really want your son, will know why and where they see him. Those that are looking for a BP pitcher, or bullpen catcher are usually more vague
Generally, I would gravitate towards the coaches that really love your son as opposed to those that seem to take him as an afterthought. This is tricky, because so many young men let the prestige of playing for a certain school blind them to what the coach is really saying or really feels. In short, better to go where you are fairly certain he'll play, than where he has a minimal chance to see the field. The coach that loves him is more likely to play him.
Ask about offseason and in season practice schedule. How many of his players graduate on time, or at all. Unless your son is getting a full ride, you'll be paying 20k per year for the "privilege" of playing each extra year of ball if he doesn't graduate on time. Of those who graduate, press to find out how many are getting real degrees, how many of his players are graduating with basket weaving and Physical Education degrees.
Also, try to find out how many who have not gone on to become MLB all stars have real careers. This is important, because some coaches talk a good game to parents about academics, but once your son gets there, the pressure will be to sacrifice all to practice and play ball. In several sports, I've known athletes who were told by coaches to drop their major, because it was interfering with the sport. At the end of the day, it's the minority of MLB players who will be set for life because of their contracts. Your son's degree, is most likely what will really matter!
How many JUCO players does he regularly recruit, and of his starters how many were recruited as freshmen and how many as Juco's. Pay attention here, because some coaches will mainly play Juco's and recruit freshmen to help the team GPA.
Ask about pitching and hitting philosophies. Look for the coaches that are not trying to produce cookie cutter hitters and pitchers. If your son is looking to be drafted, then how many players actually get drafted from this team. Better to go with a program that regularly sends guys than ones that don't. You'll find that there are programs in D1, 2, 3 and NAIA that regularly send guys and ones in all divisions that hardly or never do.
The mistake that is regularly made in my area is that players are so captivated by a D1 program, especially the SEC and SoCon schools, that they ignore all the warning signs. Lots of great pitchers (90+ guys) and great fielders and hitters never see the field and either drop the sport or transfer out after their first or second year. Others end up in a school that doesn't have the major they wanted, and so they transfer. And still others leave because the actual school and or social environment was not at all what they wanted.
And lastly, make sure your son would go the school if he were to drop baseball. Lots of guys get recruited, and decide college baseball is not for them after a time. Once you start the transfer game, it gets very expensive as schools find all sorts of ways to reject another college's courses, so they can charge you for more classes at their school.