No, Javascript is not "a more popular language for game networking". It's a more popular language for webpages.
I think perhaps we're using different terminology than you are, and because of the terminology confusion, you might be getting confusing results from your web searches.
When someone says "game networking", usually that refers to a game Client that talks to a game Server (like how World of Warcraft, League of Legends, or Modern Warfare's multiplayer works). Internet "packets" (blocks of data, similar to files saved to a harddrive) get sent between the Client and the Server to communicate information between them.
Whatever language the game client is written in, the same language is used to send and receive packets on the client's side.
Whatever language the game's server is written in, the same language is used to send and receive the packets on the server's side.
The server (and the server-side networking) could use pretty much any language. Javascript would work, but is not the most popular choice, and in many situations would actually be a bad choice (depending on the nature of the game).
As for the packets themselves, they could be described using a Domain Specific Language to generate the code for the packets, but they don't have to be and often aren't. Sometimes the packets are written out as JSON or XML or another markup language. They don't have to be and often aren't.
Javascript, while used for many purposes, is most well known for running web pages in a web browser and occasionally doing server-side processing as well. This is an entirely different category of applications than game networking.
What language are you making your game's client in? Java? Then use Java for the client-side networking.
What language are you making your game's server in? Java would work - I'm not a huge Java fan, but it would work. Javascript wouldn't be much better.
Servers require alot of performance, depending on the nature of the game and the number of people connected at once and the hardware it's running on.
C++ seems like the best choice for that, but I'm biased in C++'s favor.
If I were in your position:
If your game is a larger project, I'd look into using C# (running on MONO - you'll want the server to be able to run on Linux) to write the server since you already know C#. I think C# would be better suited for a server than Java, but that's a hunch on my part - I'm not aware of any C# MMO servers.
If your game is a smaller project, then I'd just write it in Java, because one major benefit of writing the server in Java is sharing code between the client and server.
Disclaimer: I'm speaking from accumulated knowledge rather than actual experience - I've read alot about these subjects, but haven't actually written a networked game before.