Hi scubadave
We did diving Krakatau when we lived in Jakarta 3 years ago. Nice site, underated. Being local, we arranged everything ourself. Krakatau can be reached within 1 hour with speedboat form Marina anyer - 1.5 hour by car from Jakarta if you start early morning.
Not many operator offer daily trip to Krakatau - the sea can be very chopy, you'll need powerfull speedboat. Don't use small wooden boat.
There's lot of nice accomodation in Anyer - our favourite is
Hotel Java - Anyer (Indonesia): Sol Marbella - Sol Meliá Hotels & Resorts.
I don't think this resort has diving operation but I believe they can also arrange diving trip to Krakatau. Or you may contact
Planet Diving Indonesia :: Diving In Jakarta Indonesia - they can offer day trip - normally during week end to Krakatau, Shangyang, and Ujung kulon.
To my knowledge, the only LOB serves western java is Cecelia Ann
Java Sea Charters based at marina anyer. Never use them so can't comment their service.
Re,. Jakarta safety issue - with 12 million people typical big city there's always an unsafe place particularly if you walk alone with Rolex watch or gold nekclace. We lived there for many years and even regularly visit jakarta every year; there's thousand expat live there too, if you are interesting with their view, check
Living in Indonesia, Site for Expatriates-Jakarta Indonesia
Let me know if you need more info
Cheers