Wow thanks for everyone who responded! I should also probably mention that he is working in a genetics lab this summer. The lab head mentioned to me yesterday that the research assistants all use Python for their genetic analyses.
So it sounds like it might be a good idea for him to learn Python. I do understand the arguments for Java and C++. My son is only in grade 9, so it probably makes sense for him to do Python this summer, and then if further interest develops, he could learn Java and/or C++ later.