Pattimura Airport is 37km round the bay from central Kota Ambon.
Hatu- and Liliboi-bound bemos pass the airport gates (10,000Rp, 70 minutes from Mardika). There is a ferry (per person/motorbike/car 2000/5000/20,000Rp) across Teluk Ambon to the airport side of the bay. If you time it right and use the ferry and an ojek, it would be comfortable and inexpensive (80,000Rp), so worth considering. A taxi costs up to 200,000Rp to/from the airport. A new bridge is expected to connect the airport directly with the city centre; at research time it was still incomplete.
There is also an airport bus that leaves from landward side of the Peace Gong four times daily (4.30am, 5am, 10am and 1pm – timed to feed airline departures). It departs from the airport for the city centre after the inbound flights land (approximately 7am, 8am, 1pm and 4pm).