By train
Information about train tickets from PT Kereta Api Persero is available on the Web, but no on-line reservation is possible. In Jakarta, you can buy your tickets in the major stations up to 30 days in advance. Except on weekends, you can generally buy a ticket just before departure. Beware of ticket touts! They will offer their wares even to people waiting in the queues in front of the ticket sales points. You should expect to pay 50-100% more if you do so, and you might find that your coach has empty seats anyway.
Jakarta has several train stations.
By bus
Passengers from other cities arrive in bus terminals such as Rawamangun East Jakarta Kampung Rambutan Southeast Jakarta, Pulo Gadung East Jakarta, Kali Deres West Jakarta or Lebak Bulus South Jakarta. You'll need to speak at least functional Indonesian to manage, and the terminals are notorious for muggers and pickpockets, so observe the safety precautions under #Stay safe.
By ship
The national ferry company, PELNI, and other sealines, operate passenger services to destinations across the archipelago from Tanjung Priok port in the North of the city. Some smaller speedboats, particularly to the Thousand Islands Pulau Seribu, depart from Ancol also on Jakarta's north shore.