I certainly agree that it is hard to see people in the water but almost everything is a reflection of the speed at which the vessel is moving. Going slow (no wake) will allow you to stop or change direction prior to making any contact with someone in the water. In my opinion we should have a 600 foot no wake zone on the east coast all the way up to the marker in habaneros. Furthermore, we should advise swimmers to stay around the docks and designated swim areas and be vigilant that should leave a fairly good size safety zone.
There is absolutely no reason that this could not be done. The Port Authority should allow residents to use photographs to report violators. a series of about 20 - 25 buoys would be enough to cover the area in question.
Telling people not to go in the water without a licensed tour guide is a simplistic approach that will be seen as another policy to get tourists to go elsewhere.