Not a manned boat, but it seems obvious that they would want to have another unmanned boat with instruments recording the landing event. This could be much smaller and thousands of meters away from the landing site so there would be very little risk of it getting inoperable by the landing rocket.
They keep people in the area where rockets liftoff and land (a few kms away) and besides, they launch rockets in space, do you really think they lack the technology to, for example, send the video feed to another ship waiting at a few kms distance?
Would you keep manned boats in the area where a rocket is coming down?