At first I thought that Portugal would pass to a Spanish Infante but when I looked into it I realized that all the Portuguese Infanta's were unmarried, dead or married to a Portuguese infante at the time of their flight to Brazil. Even the Spanish infante Gabriel's by Teresa of Beirason, Infante Pedro Carlos, was with the Braganzas. Thus if a catastrophe sank the fleet and killed every last Braganza while en route they'd have to go back quite a ways to find a legitimate successor.
Beacause most of the infantes and infantas of the 18th century tended to either marry their neices or nephews or never marry at all there are few descendents outside the Portuguese royal family. As far as I can tell you would have to go all the way back to John I, the 6th Duke of Braganza whose daughter married the Duke of Escalona. So I suppose theoretically the legitimate claimant would be Diego, 13th Duke of Escalona.
However the Dukes of Escalona were Grandees of Spain but not of Royal blood, and neither were the Braganzas at the time of the marriage so he doesn't even descend from a Braganza King merely a Duke of Braganza. Those two facts combined with the distance of the claim and the Duke's Spanish nationality make for a pretty tenuous claim.
I would have considered descendants or natural/illegitimate children but there weren't any living by the time in question. So the only other option would be to go back to the death of Sebastian and pick one of the other contenders for the throne that emmerged at that time.
1. So we'd have the descendents of Manuel eldest daughter Isabella, namely the Spanish Habsburgs, or at least their heirs. There's some dispute over the true heir to the Spanish Habsburgs. Theoretically the marriage contract of Maria Theresa of Spain never mentioned her renouncing the Portuguese throne, likely because the Spanish Habsburgs were no longer claiming it. So their claim should pass to the Bourbons. This would give us the descendents of Philip V of Spain. This leaves us with a son of Charles III of Spain. Or perhaps Charles, recently deposed King of Etruria, descendant of Philip, Duke of Parma. Or Cardinal Luis de Borbon, Count of Chinchon, son of Charles III's brother the infante Luis.
1A. One could interpret the claim conventionally passing to the eldest male child so that would mean it stayed with the French Bourbons and thus Isabella's heir would be Louis XVIII of France.
2. Descendents of Beatrice, second daughter of Manuel I. These would be the Dukes of Savoy and their cadet branches, namely the Princes of Carignano. They're currently ruling from Sardinia have lost Piedmont-Savoy to Napoleon.
3. Descendents of Duarte, Duke of Guimarães, youngest son of Manuel I. OTL this was the origin of the Braganza claim as Duke John I of Braganza (himself a descendent of a natural son of John I of Portugal on his father's side while his mother was sister to Manuel I) married Duarte's second daughter Catharine. So the Duke of Escalona could trace his claim thusly.
3A. Descendents of Duarte's eldest daughter Maria. Technically this was the best claim but it was not pressed because Maria married the Duke of Parma an ally of Philip II of Spain. Through that marriage her claim eventually passed to the Farnese heiress Isabella who married Philip V of Spain. So Philip V's descendents can, like the Braganzas before them, trace their claim both matrilineally and patrilineally. Interestingly the matrilineal claim descends from a son of Manuel I and the patrilineal claim descends from a daughter of Manuel I.
So reviewing the claimants Louis XVIII is out as it would mean a personal union that no one is interested in. The Duke of Escalona is a grandee of one of the other claimants. Vassalage didn't stop the Braganzas but said Grandee is stuck in the middle of French occupied Spain so Napoleon will simply imprison him if he gets ideas.
The House of Savoy actually has few available candidates. Charles IV Emmanuel has abdicated by this time, but he has no children anyways. Victor Emmanuel I has only daughters making his only surviving brother, Charles Felix, his heir presumptive. Charles Felix has only just married and has no children of his own. And the only surviving male in the Carignano line is the nine year old Prince Charles Albert (future King of Sardinia since the first three will not end up producing an heir). Sure they have daughters to pass on their claim but so do the Bourbons. The real problem is they have no one to claim the throne in 1807.
Thus it seems like the Spanish Bourbons win out. So then it just becomes a question of which one. The Spanish Royal family has been interned at Valencay in France as is the Duke of Parma/King of Etruria. The only ones that have freedom of movement are the ones ruling in Sicily with British protection. So it's possible that one of Ferdinand III's sons is made nominal King of Portugal in order to put someone at the head of the Portuguese Empire. Only problem is his second surviving son, Prince Leopoldo, is only 17 years old and because Ferdinand's heir Francis hasn't yet produced a son of his own Leopold is still second in line to the Sicilian throne. So the British could send him to Brazil but he'd need some kind of Regency. A Regency of Britons and Italians isn't likely to be popular or successful in Brazil.
It seems more likely that the Portuguese Empire falls apart with competing claimants trying to govern it from afar, much like the Spanish Empire. It will then be left to the Congress of Vienna to sort out the Portuguese succession after Napoleon is dealt with. And at that point even given the reigning principles of legitimacy and restoration the powers could do just about anything they wanted. So if its not a Spanish or (Two)Sicilian Bourbon it could be anybody as long as they're a Royal and Catholic.