There are many autonomous boats, but they all do the same thing, driving circuits around a lake. 

Watching a guy trying to repair a foundation from a boat revealed the biggest need is a boat which can hover in the same position like a quad copter.  There was also the phase where SpaceX tried to catch fairings on boats, but they could never get the boat agile enough to do the job.

It's hard because station keeping requires 4 thrusters.  Quad copters were originally hard, but eventually the world got used to 4 propellers.  The thrusters on a boat have to thrust in 3 directions, while the thrusters on a copter have to thrust in 1 direction.  There's a long lag time for a boat thruster to turn, then thrust.  A boat encounters a lot more drag when it tries to move fast in any direction.  

The problem is more easily solved by having a quad copter that floats, but a floating quad copter wouldn't do any good for foundation repairs.  Part of the problem is easy.  Press the boat against the foundation with a static force.  There could be a force sensor which causes the motor to exert a constant force.

Station keeping in open water is still required for fishing tools out with a magnet or dredging.