I prefer Java over .Net because I do coding on a variety of platforms -- Windows desktop, Linux/Apache/MySQL/PHP web server, Android phone and Mac multimedia desktop -- and I want to be able to write code for all of them. Since Java became my programming language of choice I never looked very seriously at the Windows-heavy development options.
In the early days of Java it didn't do a great job of presenting user interfaces on Windows that were competitive with what you could do using Microsoft's programming tools. It was always obvious you were running something written in Java.
The "Java vs .NET" question is one of those old questions that people can debate endlessly over without ever reaching a clear conclusion.
It's really comparing a screwdriver to a hammer. Which one is better? It depends on the job you need to do, and neither is clearly always better than the other.
There are many reasons to choose one over the other. Companies like Java because it's cross-platform; it's very easy to run it on Windows, Linux or whatever operating system you want to use. Companies like .NET because they might have invested in Microsoft's enterprise software stack, so .NET from Microsoft is a natural choice.
Without knowing anything else about your IT environment, it's impossible to say which will suit your organization better.
Sometimes young programmers ask "should I learn Java or C#, which will give me better career opportunities?". That's also a question that is very hard to answer.