Is there risk of malaria on a boat trip?

Not really. Malaria exists in Indonesia, but being a mosquito-transmitted disease, and since there are no mosquitos out at sea neither on board, it is very unlikely to get infected during a boat trip. We don’t know any cases of malaria during boat trips.
Nevertheless we recommend you to seek medical advice about tropical diseases before traveling to Indonesia, and if needed take proper medication.
BTW, it is recommended to have an up date of your vaccines against tetanus, hepatitis, etc.