C# is great but I am curious to know specific teams using Java at Microsoft. I know about LinkedIn but one can't jump from Microsoft like internal transfer to other teams / orgs.
You won't find many teams using Java. Definitely not the hard core Java teams other than few teams dabble with open source tools or libs. Why do you care about the language? C# is the primary language used for backend services and C# is much better language than Java. (And I just started a holy war)
Find a team that maintains libraries for other developers to use services. They probably maintain a Java one because of its ubiquity
Not many companies uses .net. so .net Is a tribal knowledge which one can learn by being at Microsoft for long. When Microsoft hires people from outside, they need to compete with people who have this tribal knowledge of .net and related technologies.
Or Scala
No one uses Scala for anything serious
Twitter does for sure.