I'd expect to see more Java shops in SV because Java's huge open source ecosystem makes it a much better platform for doing, for lack of a better term, "tech company stuff." Also, SV is heavily influenced by academia, where .NET was just a flat-out no go for a long time because it only really worked on Windows.
But I see a lot more .NET for the kinds of in-house enterprise development jobs you see in regions like the Midwest. For that kind of work, there's usually not much in Java that you can't get on basically any other platform, too, and .NET/C#'s better ergonomics will let your team be more productive at the kinds of stuff they're doing. (I'd bet Clojure is even better still, but Clojure doesn't look good in khakis and a polo shirt.)
Joda Time, Apache Commons & Guava, Jersey, Hibernate, etc. - heck, even Dropwizard - are all libraries whose .NET equivalents are just different bits of .NET itself. Similar for Java Mission Control, for that matter.
Where .NET pales, IMO, is for stuff like Hadoop that, while astoundingly helpful for some problem domains, isn't so useful for most enterprise development work.