The exact calculation depends on the ship and cargo size and current value. The fact is also complicated that while Portuguese had a virtual monopoly of importing spices in the 16th century via the Cape route, in 17th they were (not so) slowly pushed out by the Dutch, with English and the French also joining in eventually.

But still, the answer is clear: the cargo of spices was more valuable

Spices could be very valuable. In a previous answer of mine, I analyzed the profitability of Magellan's expedition of 1520s, and I showed that a single ship that managed to return to Spain with a batch of cloves (which were among the more valuable of spices, compared to pepper which was the lowest in value) and basically paid of the entire expedition which included paying the buying and equipping of 5 ships (other 3 were lost, one deserted and returned to Spain and is not looked at) and the provisions and crew wages!

Another great source for you is Decay or defeat ? : an inquiry into the Portuguese decline in Asia 1580-1645 by Ernst van Veen, who analyzed the profitability of Portuguese and Dutch voyages of around year 1600. Most relevant are chapters 3 (Portuguese), 7 (Dutch) and Appendix (Tables and figures)

In it, you can find an approximation for Portuguese cost of carrack that can carry 1000 toneladas of cargo to be 50,000 cruzados (Portuguese gold coins) but the prices fluctuated widely. At the same time, pepper (the cheapest commodity) could be sold in Europe at prices of 28-45 cruzado per quintal (around 51 or 58 kg). If we account for losses and round down that 1 tonelada can fit 15 quintals of pepper, each quintal being worth minimum of 28 cruzados, we get that a 1000 toneladas carrack can have pepper on board worth 420,000 cruzados, almost 8 times the worth!

Of course, the investors had to pay the merchandise, the losses, insurance etc. but to quote the linked text:

From the very simplified calculation, one might conclude that, even in the bad years of the 1590s, the Casa da Índia made 43 percent and the Asia contractors 29 percent on their investment!

ANd that's with the buying and equipping of ships.

The same source is even better for the Dutch, as we know the exact cost of their ships.

From Appendix 7.1 and 7.2 we see that the Dutch paid for outfitting cargo ships around 2.1-2.4 kg of silver per metric ton of freight. At the same time (from appendix 7) pepper could be sold in Europe from 24.5 grams of silver per kilogram at the beginning, quickly falling to 16-17 grams of silver per kilogram. That means that a single ton of freight consisting only of pepper would be worth 16 kilograms of silver.

So for the cost of outfitting (which would mirror the value of the ship) of 2.4 kg of silver per ton, the cargo would be worth at least 16 kg of silver per ton. That's like 6-7 times more valuable!

In the same appendix tables, we can see that even in outgoing voyages, when ships didn't carry spices but normal merchandise and money like silver, the value of the cargo was the same or at least near the value of the equipping of the ship, so even the normal value would be roughly equal in worth with cargo,