Never do certifications for software engineering. The only certifications worth a damn are security certs and networking certs. If I saw a programming-related certification on a resume, I would completely ignore it since the only thing it tells me is that you paid some money to get a cert.
While I'm not a fan of Java, it's most certainly not a dying language and you will be able to easily find employment into perpetuity. If I had to pick, I'd personally choose Java over .NET purely to avoid being trapped in Microsoft-land, especially with all of the bullshit they've been up to lately.