My best bet would be Valencia. From the 1350's to the 1500's it was the economical center of Aragon aswell as it's largest city and sometimes the capital (The crown of Aragon didn't have a proper capital like France had Paris or England had London, fixed capitals in the late middle ages were the exception, not the rule), as well as also being the scientific and literary center of the Crown, hosting the first printing press in Iberia. Valencia is placed in a fairly large plain which could easily substain a large city and close to a good fish reserve in the Albufera Lagoon. However it has it's problems, mainly that the city and it's surroundings have a large muslim population (30% of the Kingdom of Valencia, if I recall correctly) which could pose a problem if they're not expelled, and if they are Valencia will surely lose importance.
Saragossa could work, but it's not as centric and it was considered the Aragonese capital, I guess Castilians wouldn't fit so well there (remember Castile alone has roughly the population of the whole crown of Aragon). Saragossa has the Ebre and it's floodplain which is fertile but not as fertile as the Valencian plain. Other cities in Aragon like Barcelona, Tortosa or Tarragona could work as well, I guess Barcelona is your best bet given it eventually gained supremacy amongst the other Catalan cities. Pamplona could also serve, but by the late 1400's it was still it's own kingdom, and the city is too close to France for security.
Options in Castile include Cuenca, which is probably the most centric but has some limitations due to it's geography; Murcia, which was the capital of it's own kingdom within the Castilian Crown (and Aragonese for a brief time); Toledo, the historical capital of the Visigothic Kingdom, but kind of too close to Portugal-Leon (doubt that mattered the Aragonese-Castilian Union as they would attempt to seize the territory at any time); and Burgos, which by the time was fairly large and home of the Castilian wool industry.