First, I must say that killing the squid on the surface of the water is unlikely due to the sheer size of the squid. However, if you repeatedly injure it, it will either die, decide not to bother you, or have to wait to heal before striking again.
Find a cliff facing the sea. Now use boats and ranged weapons to lure the squid over. Now shoot at it from the cliff, attracting it to come as close as possible to the cliff. Now light the fuse and toss the barrel over. Repeat.
Requires some sailors to sacrifice themselves. Load a ship with explosives. Now get the ship as close as possible to the squid, and set it off. Might not kill the kraken, but will injure it.
The Fish Pile
Go back to the cliff setup, but dump fish into its mouth. Hopefully it keeps its mouth open long enough for you to throw explosives, or whatever you want to throw at it, at it.
The Large Spiky Ball
Cliff setup, but spiky rocks as well as explosives. These will puncture the creature's skin. A lot.
If you're at war with another coastal nation...
Use your ships to lure the squid over to the opposing country and their ships. Now it's not your problem anymore.