You forgot of:
He's a master of Java Programming.
That's the preposition used in the famous idiom Jack of all trades, master of none. It also seems to be the preposition of choice according the Ngram:
As to your note:
Java programming is just an example and not something to explore or dig in further. I'm concerned with when you master something, you master at or in that?
I believe there are some things that one can master, and one preposition will sound more natural than another. For example:
James is a master in deceit.
Dave is a master at forgery.
If – for some reason – a writer did not want to use of, then at seems to work a little better than in when referring to dextrous skills where you make something tangible (such as forgery, woodcarving, or quiltmaking), but in seems to work a little better than at for something more abstract (such as deceit, inspiration, or strategizing). There's no fixed rule about such matters, though, and prepositions tend to be very flexible in usage.
What would work best with "programming"? Probably of.