Your experience and comfort level with a language should play a large role in your choice.
If you have previous experience with C/C++ Linux development and are comfortable with using it as a development language, you should find the differences marginal.
On the other hand if you lack any previous C/C++ Linux development, you may want to consider Python which is the next widely used language out of the three.
Of course Bonescript should be easy enough for you to learn and can be used to quickly development many simple tasks.
At this point in the game, I tend to avoid the need to familiarize myself with new niche languages and utilize my decades of experience with C/C++ and fallback on scripting languages like Python if need be.
Although this is my personal preferences and may not be the optimal choice for yourself.
You may find it advantageous to get your feet wet with Bonescript and after you have familiarized yourself with the BeagleBone Black platform branch out with Python or C/C++.
Either way, I am sure you will find the BeagleBone Black as great development platform as I have.
I just ordered my third unit and several more capes.
BigDog