I thought of that too, but it seemed just as awkward as the original, to my ears. How about

After eight years of excavations, archaeologists have uncovered remains such as peppercorns, wine, beads, sapphires, and teak and metal from the remains of the ships.

I didn't read this particular article, but I have read others similar to this and am assuming that the remains were found in sunken ships that are currently being excavated. Is this the archeological site that was once a harbor and is now found on dry land?