Towards the late Middle Ages crew of a European ship could be paid in one of roughly two concepts: they could either get a predetermined amount of money, like a labourer, or they could get a percentage of the success of the voyage, like a minor partner in the venture . The former would eliminate the risk for the crewmember and make sure they get at least something, but the downside was the pay wasn't much. And the latter would enable a possibility of higher profit but could just as well mean ending up with zero money.

By the eve of Age of Exploration it seems the preferred way has leaned to the first option, where crew would get a fixed sum or a monthly wage, but additionally they would also get some cargo space where they could carry trade items, in a way indirectly enabling the men to earn more money for themselves.

Spanish

The abundance of interest and research that from earliest times focused on Columbus' voyage to America amassed a wealth of data. One of the relevant documents is the muster roll of the 4 month advances Columbus gave to his crew, which you can read here.

The list isn't complete, but we have enough data that we can see that most ordinary mariners got a wage of 1000 maravedis per month (4000 advance for 4 months). Ship's boys, or junior seamen got 2/3 of that amount, or 666 maravedis per month. If the advances followed the same ratio as for the sailors, we can see that the pilots wages were 1.75x or 2x higher then for the mariners, the same went for the master and other higher officers, while a captain (of the Pinta, Martin Alonso Pinzon) got 4x the wage. The level of discrepancy between the captain and the men is here unusually low, and with time the difference would rise substantially

The base pay mentioned, of 1000 maravedi per month for ordinary seamen is confirmed by documents from other sources. Magellan had to raise the offered wages to incite men to sign up for his expedition, but he could only offer the wages of 1200 maravedis for mariners, 800 for junior seamen and 500 to pages, a very minor increase.

By the late 16th century the wages either stagnated or rose slightly nominally to 1500 maravedis per month, but rose less then for other professions. Pablo E. Perez-Mallaina in his book Spain's Men of the Sea: Daily Life on the Indies Fleets in the Sixteenth Century (which I highly recommend btw) gives a comparison of wages and we can see that sailors earned much less then craftsmen in cities, even when we account for free food they received. They did receive wages similar to soldiers though, as wages of Spanish pikemen was 900 maravedis per month and arquebusier earned 1200 maravedis per month. To get a insight in how much that wage could give you, here is a list of common item prices in 16th century compiled by Perez-Mallaina.

For the officers, the situation gets harder to clarify. The highest officials didn’t get paid monthly, but usually for the whole voyage, with a traditional advance. For example, Spanish pilots going to America and back were to be paid between 40,000 and 50,000 maravedis per completed trip.

Portuguese

In addition to Spanish data, we have some Portuguese data. According to Gaspar Correa, 16th century Portuguese writer, who admittedly is slightly unreliable, for Vasco da Gama’s voyage King ordered higher salaries to be paid. The Able mariners would get 10 Portuguese Cruzados, which would convert to 3400 maravedis per month, able seamen would get half that that, at 5 cruzados or 1700 maravedis, pages one thirds of mariners pay at 3.33 cruzados. Captains of the fleet would get 1000 cruzados (340,000 maravedis) for the whole voyage, and master and the pilots 500 cruzados. Boatswains, mates and minor officers would get 1.5x the mariners pay, while specialized craftsmen like caulkers, carpenters etc. would get 2/3 of the mariner pay.

Importantly, in addition to this wages, they were also allocated some pepper from the hold, and a space on the ship (in the form of chests) where they could carry their own stuff. The amounts were also divided in similar ratios like the sums of money.

If wages of Vasco da Gama’s expedition were high, they didn’t stick around till end of century. According to Jan Huygenvan Linschoten in a work published in 1590s, Portuguese crew wages on Indian Armadas dropped significantly. Able Mariners earned 1000 Reis (2.5 cruzados, or around 900-1000 maravedis at the time) per month, oridnary seamen earned 666 reis, pages 443 reis. Carpenters, coopers etc had now 1200 reis per month, while masters and the pilots got 120,000 maravedis (300 cruzados) per trip. Again, the key incentive was actually the allotted space one could use to ferry items and conduct personal trade.

 

I hope this made some sense, I had to go around and get data from numerous sources, and I might have made it more complicated then it should be.