Sure! I read somewhere that after Dias crossed the Cape of Good Hope he wanted to carry on all the way to India but the crew didn't feel the same. I can't remember where I read it or if this is trustworthy but in any case the decade-long gap between the trips of Bartolomeu Dias and Vasco da Gama shouldn't be a fatality: we can easily imagine an expedition to India being organized in the early 1490s.
Furthermore we can always find ways to delay the expulsion of the Jews. Princess Isabel died in 1498 IOTL. Had she died a little earlier, king Manuel is still likely to marry a Spanish princess and expel the Jews but the process will be delayed.
He'd probably marry Maria of Aragon as in OTL - she was a little young to be married in 1497 or 98, so the expulsion of the Jews would be put off until 1500 or so.
We don't really need such a delay, though - if Dias convinces his crew to go to India, Zanzibar would be in Portuguese hands before the 1497 expulsion. Once da Gama found the India route, Portugal acted very quickly to secure way stations, seizing Zanzibar within six years of his expedition. Assuming a similar timetable after a successful Dias voyage, Zanzibar would become Portuguese in 1494, which would give Jews time to settle there if Manuel adopts a policy of tolerating them in the colonies. As an added bonus, Dias' success would give São Tomé added importance as one of the way stations to India, meaning that Portugal would want to establish a settlement quickly, and might use Jews if (as is likely) there aren't many Portuguese Catholic volunteers.
So a 1488 POD involving Dias' success, with a secondary POD involving an earlier death for Dom João (from a fever brought on by contaminated Indian goods?) might see small but thriving Jewish communities on Cabo Verde, São Tomé, Zanzibar and possibly Madeira early in the 16th century. The Atlantic communities would include agriculturists, craftsmen and merchants, but the one in Zanzibar would be almost entirely mercantile. The Zanzibar Jews could then spread to the cities along the Swahili coast, especially if the Portuguese crown decides to expel them from Zanzibar at some point, and intermarry with the Africans to create a semi-indigenous population similar to the Afro-Arabs of the same region. Now I'm imagining some 19th-century mestizo Jewish landowner-adventurer becoming this timeline's Tippu Tip, and liking the idea much more than I really should.
The Church was extremely active in East Timor and would not have taken kindly to incursions of a non-Christian variety on their designated selections.
And... assuming OTL (you really don't change much outside of Portugal's Jewish policies with something like this), the Javanese are going to put any such community through a meatgrinder in the 70's.
If you change Portugal's Jewish policies, you change the migrations of the Jews, which changes the history of every country in which Jews played a part. Definitely no Spinoza, probably no Rothschild or Mendelsohn either. This is a POD whose effects would be very subtle at first, but by the 20th century the world would be changed out of recognition.
During most of the last quarter of the 16th century and about the first half of the 17th the two countries were in a 'personal union' under the Spanish Hapsburgs, and this was accepted in most if not all of the Portuguese colonies too. The Treaty of Tordesillas meant that Spain couldn't just have the colonies transferred to its own ownership, but a royal decree from the king in his 'King of Portugal' role about the presence and status of those Jews would have been legal enough.
I'd mentioned the personal union myself earlier in this thread, so there's no excuse for me forgetting it now. But if we're messing with the Portuguese royals, the personal union might never happen. Maybe there will be no Sebastian to get himself killed in Morocco, at least without begetting an heir first, or maybe one of the other claimants will win out over Philip of Spain.
Or if the union still happens, Portugal would suddenly inherit all of Spain's enemies as in OTL, and the English and Dutch would start to pick its empire apart. It wouldn't take a very big fleet to grab São Tomé.