Wow, that's a lot more information than I expected on the topic, awesome.
This is interesting. I was initially interested in Mahapahit because it was a Hindu Empire in OTL Indonesia. I am not too familiar with the process of Islamicization because I haven't come across many books that give it any credit in detail (often just a passing "well, there were Arab traders so they became Muslim).
I think there are ways to at least delay the Islamisization of the Malacca Strait. Perhaps Mahapahit could survive simply survive by Islamisizing though (in the far future), I'm not really sure (and have no preference it's all incredibly interesting).
This is from wiki: I'm not sure what to make of the source (and its validity), but if we just take the assumption that the Hindu king of Malacca does not decide to convert to Islam. I doubt Islam can be kept out forever, but it's certainly possible that a reasonably strong Hindu kingdom around the Straits could really diminish some of the influence of Islam for a short period of time.
This might provide a sort of window of opportunity to insulate a more successful Mahapahit- but my historical knowledge of Indonesia is really poor, so it's good we have some people here who really know their stuff

.
As an afterthought, I imagine a more successful conquest of West Java would have some butterflies, which might blow away the Hindu king of OTL in Malacca- but I imagine the question of conversion really remains so perhaps it's still relevant.