There are daily flights from Jakarta to Ambon, either direct or via Makassar or Surabaya. Garuda is the airline rated safest internationally.
Alternatively there are boats from various parts of Indonesia. Schedules change frequently, but any travel agent in Jakarta or a major Indonesian city can arrange this.
The airport is located in Laha, 45-minute driving from the city. DAMRI bus (costs IDR 35,000) connects the airport and the city with fixed schedule four times a day. City to Airport (04.30, 05.00, 10.00, 13.00) Airport to City (07.00, 08.00, 13.00, 16.00).
The bus leaves the city at the peace gong on Jl. Sam Ratulangi at the big electronic advertising sign.
Taxi costs IDR 200,000 for one trip from/to the airport.
Red Bemos run from outside the airport gates to Kota Ambon for less than 15,000Rp. Ask the driver if he goes the full way to the city center, as some of the Bemos stop half way to the city center and return.
The "FRiS Fresh Market" supermarket on Jl. Rijali close to the crossing of Jl. Pituina has a good range of cold beer.