Thanks for reposting with the correct construction.
To be "off Sheerness" means that the boat was in the water a short distance away from Sheerness (a town in Kent, in the south-east of England). "Lunch came in" suggests to me that lunch was ready, or was delivered by one of the three men on the boat. If it's a fishing boat, it's possible that it means that they caught some fish just in time to eat them for lunch. I've never read the book so I don't know the rest of the context.