I’m pretty sure that is the harbor outside Steveston, BC, where the set of Storybrooke is based. I have a feeling that Captain Hook has finally come to SB on his ship, the way that Peter Pan flew Hook’s ship to London using a little bit of pixie dust.
I would LOVE it if Hook makes a grand entrance to SB on his ship! Just coz they’re shooting near where SB is though, doesn’t necessarily mean that the area they’re shooting is also meant to portray SB, it may have just been the easiest place they could set up a shoot with a big ship. But it’d be really cool if the ship is in SB.