The dock isn't far from the Queen's Wharf restaurant seen earlier in the same episode. And it's less than two miles southeast of the Coral Cove marina where they filmed LaGuerta talking to the harbor master.
However, earlier (undated) Bing aerial photos show the Fearless docked at the nearby Pier C:
The initial driving scene (of Caffrey driving into the port) was shot on the Pier (D) to the east of the ship.
In the screencap below, the car is headed west on El Embarcadero Street, approaching Pier D Avenue West.
This Google StreetView matches the scene (except for the large ship seen on the horizon).
How the heck did you figure out where it was?
A. The initial tip came from Rick, who let me know that they were filming aboard a ship down near Pier D.
After the episode aired, I got an email from a fan, Todd Milyard, who told me that the ship appeared to be a U.S. Coast Guard Cutter, and sent me this photo of a similar ship. The resemblance was striking.
But I needed to find out which of the 180-foot 39 Coast Guard Cutters it was.
I emailed Scott Price,
a Deputy Historian at the U.S. Coast Guard Headquarters, sent him
screencaps of the ship taken from Episode 9, on the longshot chance
that he might be able to identify it.
Scott confirmed that it was definitely a US Coast Guard buoy tender, 180 class, and he pointed me to a post on a website that said that the Sorrel has been used in a recent Starbucks TV commercial, and which also reported that the Sorrel had been renamed the SS Reliance.
I attempted to track down that Sea Scouts ship, I learned that it has
been sold again, and found at least one mention of a ship actually
named the Fearless. Even more Googling ensued, until I eventually found a post from someone with the username "BuoyJumper", who stated that the Fearless was owned by Seaway Marine.
I then started Googling for "Seaway Marine", and eventually turned up their website, which gave me the story.
You can read more about the history of the Sorrel (and Coast Guard buoy tenders in general) here.
( Thanks to everyone who helped: Rick, Todd, Scott and "Buoy Jumper". Thanks guys! )