Do you like driving a car or flying a plane? Both are technically capable of transporting you but they are rather different beyond that. Unless you meant Java which is a more conventional programming language. I will do all three.
Javascript aka ECMAscript is mostly intended for web use. Browsers run it so websites can achieve more functionality. Technically as the 3ds has a web browser with a very limited javascript engine (a ridiculously limited one) you could write code for it that would allow you to play something here. There are other takes on javascript, probably the more notable being node.js, but that is an odd world and I would not suggest going there if you do not have to.
I like
https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Introduction as a guide to javascript, though how good it will be if you are starting completely cold I do not know.
You will probably also want to know HTML (pay attention also to HTML5) and CSS, possibly also some PHP, mysql and other web focused things to truly get the most out of javascript.
C++ is a somewhat high level language. Not as high a level/abstracted from hardware as Java, python and especially javascript, but more removed than plain C and assembly even if there is not a lot in it at times. C++ is exceptionally powerful and used by many of the best and brightest programmers out there* as it does basically everything short of web stuff, and even there you see a few people doing some things. The downside is it is one of the harder languages to truly get a grasp on and it will allow you to make silly mistakes that other programming languages will shield you from (usually at a cost in terms of speed) and inter platform operability (java has its runtime that works on loads of different systems, python too where C++ might need a fair bit of rework to have it run on a new platform).
I believe there is a C++ compiler that can work on the 3DS.
I am not sure what I want to suggest for new programmers going into C++, it is doable despite what some might tell you. Though if I must link something then
http://www.cplusplus.com/doc/tutorial/ , I have more for plain C but I will spare that for now.
*high performance computer games, video encoders, big boy calculation driven software, operating systems... if they are not being written in C++ then it will be because they are being written in C, something which a C++ programmer can usually fumble through and vice versa.
Java is a high level language that gained a lot of popularity in the business world. For normal PCs a lot frown upon it these days owing to an abysmal security track record, doubly so for the web plugin side of things. However it is the programming language of choice for the Android family of operating systems and there are passing popular. I am not personally a fan of Java for a bunch of reasons, and the sentiment is shared by no small number of computer types, but learn it and I would count you a programmer and you can get stuff done, including fairly high performance stuff (minecraft is a popular game written in it, it is fast enough to be used in rapid deployment/change environments and I did mention most things written for android being written in it right?).
To the best of my knowledge there is no Java interpreter for the 3ds and though there possibly could be I would not hold my breath for one, much less a useful one.