Given your limited free time in the Jakarta-area, there are really only two viable dive areas, in my opinion. One is The Thousand Islands (Pulau Seribu), while the other is the Sunda Strait. The Sunda Strait in my experience, has been a little more challenging to get to, logistically, but again in my opinion, has the better diving IF the currents are slack and viz. is up.
For convenience, most Jakarta-area divers tend to go to the Thousand Islands, which has a number of resorts. The conditions tend to be more reliable, and offers a good variety of dive sites, including reefs, a few wrecks and wharves. Sepa Island, for example, is an easy two hour high-speed ferry ride from the Ancol Marina in Jakarta. It can even be done as a day-trip if you are so inclined. The island has a dive centre and basic dive resort. The dock/wharf has some decent macro stuff. They also have a house reef, and the Papa Theo shipwreck is close by.
There are other dive resorts in the islands, but alas I am not familiar with them.
For covenience, I would recommend that you contact one of the dive ops. in Jakarta, who can easily organize a package for you at a reasonable price.
Some of the Dive ops in Jakarta which are popular with the ex-pat commmunity include Aquapro, Aquasport, Kristal Klear, and Ody Divers.
The following site has contact info. for many dive ops in Jakarta, including the first two:
Some Jakarta Dive Ops
While here is the link for Kristal Klear:
Kristal Klear
This is the link for Ody Dive:
Ody Dive
Finally, for a sample of what you might see, please feel free to visit my photo gallery and view the West Java Album.
I hope this helps.
Cheers.
Michael.