According to the module, any version, dock it. Which, yup, makes Saltmarsh a pretty decent deep water port. And yeah, 100 foot cog is freaking huge. I more chalk that up to the designers not bothering to actually look up historical ships. They got the shape right - single mast, wide body, that sort of thing, but, greatly overestimated the size.
Of course, it doesn't help that it's also an adventure location, which means that you have to make it bigger to work on D&D scale.
In any case though, you can dock major sailing ships - the food merchants that sail north to Iuz would also be a good example of this - in Saltmarsh.
-edit to add -
Naval stuff is my own hang up. I freely admit that. The anachronisms in D&D for sailing stuff just flies right up my nose. No, I'm sorry, that 17th century British Ship of the line complete with gun ports does NOT belong in a D&D setting. Since the DMG and Saltmarsh both set naval technology at about the same line as the rest of equipment, 15th century, maybe 16th century is about as late as I expect to see.
Unless we're talking Spelljammer, in which case, all bets are off. But, it gets really, really weird to see viking long ships in the same water as, say, a caravel. Those poor vikings wouldn't stand a chance. You wouldn't even need to shoot at them, just ram their tiny little boats and you'd be done with it. Grrrr. It annoys me to no end that when it comes to naval stuff, so many publishers can't be bothered to open a history book.
/me steps off soapbox.
