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Timing your trip to Maluku can be different from most of the rest of Indonesia as far as weather is concerned. In fact, even within Maluku, there are three different climate patterns in the three main regions.
NORTH MALUKU
In most of North Maluku, there are no marked seasonal differences - even my local friends could not tell me when their "rainy season" is supposed to be! It tends to be hot and humid year-round, with rains a possibility at any time. If you are really trying to plan around this, it rains a bit more during the northern hemisphere's summer. The Sula Islands follow the Central Malukan pattern though.
CENTRAL MALUKU
In most of Central Maluku, including the most popular destinations like Ambon, the Lease and the Banda Islands as well as the south coast of Seram, there is a marked increase in rainfall during the northern summer months. Travel is still possible during this time, but the seas can be more rough making travel by small boats less regular, and conditions for diving and snorkelling are less than ideal. Bring a good book for the rainy hours, but on most days there will be sunny periods, too. In contrast, the northern coast of Seram has a less marked rainy season during the northern winter, like most of Indonesia.
SOUTHERN MALUKU
Southern Maluku follows the climate pattern typical of most of Indonesia, with more rain falling during the northern winter months. The amount of rainfall here tends to decrease, and the seasons become more distinct, as you travel westwards from jungly Aru towards arid Kisar.
WIND & WAVES
Now, the above info should help you with the rain factor. However, there is another thing that might influence your holiday, and that is the seasonally strong winds, possibly causing rough seas. This may have an effect on sea transport between the islands, as well as on diving/snorkeling possibilities. Beaches facing windward may have a lot of floating seagrass or garbage washed up on their sand, reducing their beauty. Basically, the worst conditions tend to occur during the western winds' season, that starts in December, peaks in January and February, then ends in March. A less pronounced eastern winds' season occurs starting in June, peaking in July-August, then ending in September. As you may notice, between them these seasons happen to coincide with the busiest tourist seasons! No real reason to panic though. For one, these winds are never horrendous, raging hurricanes. In fact, even during the peak of the western season, conditions can be calm for weeks on end! The sea rarely gets rough enough to cause serious disruptions in transport, and even then only long-distance traffic by smaller ships is affected. The bigger Pelni ships (all except the Sanggiang and the Pangrango) almost always keep running, and so do smaller boats on shorter, more sheltered routes like around much of North and Central Maluku. The only region where you may experience more significant difficulties due to the rough seas is southern Maluku - and there you can still fly to or from the main islands if necessary. On a positive note, the winds actually make the tropical heat more bearable! :-)
CONCLUSION
If pushed hard, I would probably say that the overall best months for travel in the whole of Maluku, statistically neither too wet nor too windy, would be April-May and October-November. But that's just by the statistics, which tropical weather doesn't always follow anyway. If you can't make it during those months, don't worry too much - you can probably ignore the winds factor in much of Maluku, and just make your decision based on the pattern of rainfall, as summarized for the three regions above.
For more detailed data, you can find actual weather statistics on the following websites:
World Weather Information Service offers a very clear chart for only one place in Maluku:
Weatherbase offers less clearly presented, but more detailed and useful date for:
For the really concerned, Weather Underground offers the most detail, and on the largest number of places. You can find current weather conditions, short term and extended forecast, and most interestingly even detailed data on actual weather conditions from the past years for the following places:
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