It also depends on what you want to focus on with the students. If you want something that is already made, and has more to do with reading documentation, and plugging together /building the system and getting into the water, then ArduSub + pixhawk is a good choice.
If you want to focus more on the programming side of things or linux/sbcs, then the BBB will work fine, but you will have to do more of the system design and implementation.