Our developers use Java (mostly).
Our research department uses whatever they are most comfortable with for research, but the result of their research is coded up in C++. If we had to do it over, we'd probably do everything in Java. Misc. notes:
Personally, I am WAY more productive in Java.
I supplement Java with Clojure.
I find the performance penalty for using Java is pretty-much negligible. It's always how you do it that matters more than what language you do it in. Don't use Java Generics for number crunching though... use a dedicated primitives collection library like Colt.
Java and C++ are quite similar in some respects. I would say though, that it's easier to go from C++ to Java, than from Java to C++.
Best C++ books:
Accelerated C++ by Andrew Koenig and Barbara E. Moo
Effective C++ by Scott Meyers (make sure you get the 3rd edition)
Best Java books:
Effective Java by Joshua Bloch
Java Concurrency in Practice by Brian Goetz, Tim Peierls, Joshua Bloch, and Joseph Bowbeer
If you have to use C++, start using the Boost C++ libraries early on. You can learn a great deal just by using the Boost libraries, and reading their documentation.