How about a ballista? Physics would work like the harpoon, but it's much bigger and doesn't have a rope.
You get one shot before a five second reload, the 'bolt' flies slightly faster than the current harpoon, and it causes piercing and impact damage.
The piercing could take out about 2/3rds of a Pyra's armor (haven't memorized the stats for the ships yet), but it also pushes the target a bit, like how mines do.
Some of yall might think 2/3rds might be too much, but the slow reload would allow for a mallet strike, not to mention it'd be difficult to aim. Now you have an armor piercer for heavy weapons that has moderate range (1000m), some difficulty to use, but wouldn't tear through armor like a heavy gatling might do.