Yeah, faster and easier. Look at the diagram of the east side access tunnel - both sides of the river have extensively long amounts of burrowing underground (not underwater).
https://en.m.wikipedia.org/wiki/East_Side_Access
It's a mile just on the Manhattan side. Can't tell on the queens side but if accurately scaled it's the same - comparatively,very little is in the river.
To extend the subway from South Ferry to Redhook is almost entirely in the water if it's a single stop (not sure of their exact concept). Once at RedHook, they again could do it with minimal burrowing depending on where they want to have the station (connect from the water at the closest shore point). My guess is that if they go through this trouble, they'd want more than a single stop, but there would be ways to minimize the work with the layout while maximizing the footprint served. The length of Redhook is less than a mile, but the distance from downtown to the end of Redhook is about 2.5 miles by way of the roads, and the tunnels would have to follow the roads otherwise existing buildings' foundations could be undermined.