The entrance from the South Qeynos docks to the Qeynos Catacombs is underwater below the pier that Faren is standing on. I'm not sure which compass direction it is, but if you are exiting the boat as it arrives in Qeynos and are facing the pier it's the next pier over to your right. You might have to swim a bit from the boat.
Just look for Faren. He never leaves the pier he's standing on. He just stays there all the time fishing and being abused by Trumpy.
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