Though the Caribbean remains generally safe for cruisers, boarding and other incidents can happen anywhere.  Developing safety habits and contingency plans will contribute to a more enjoyable cruise.
The following recommendations to minimize the risk of theft, burglary and assault come from the experience of many cruisers in the Caribbean, some of whom have been directly affected by such incidents.  This list was first compiled at the beginning of the Caribbean Safety and Security Net through the efforts of Frank Zachar on Vagabond Tiger and Bob and Robin Jones on Elixir, now Buster.  The intent is not to frighten cruisers, but to identify steps that can be taken to prevent property loss or physical harm. To prevent a boarding incident from possible escalation to violence, emphasis is placed on scaring off rather than confronting intruders. Some of the recommendations seem obvious but if they do not become habits, they serve no purpose. On the other hand, if you habitually use these precautions, they become a not-burdensome routine.  The more difficult you make life for the criminal, the more likely he is to leave you and your property alone. 

1.  Avoid known high-risk anchorages; especially, do not anchor alone there.  If you do stop, use full security precautions and post a watch.  Introduce yourself to others in the harbor and decide on a VHF frequency for all to monitor.  When up at night, shine a flashlight on other boats to check for activity (only after mentioning this possibility to the other boaters earlier in the day).
2.  Whenever you leave the boat, lock/secure all access points, including hatches and ports, using good quality locks.  It's amazing what size opening a skinny, motivated kid can get through!
3.  Don't leave desirable items unlocked in the dinghy behind the boat, at the dinghy dock while you're ashore, or unattended on the beach while swimming.  In addition to the obvious outboard, this includes gas tanks and diving/snorkeling gear. Don't paint your yacht's name on the dinghy: at dinghy docks, it broadcasts that at least one person is away from the yacht.
4.  Don't leave anything valuable on deck or in the cockpit at night or when the boat is unoccupied.  Equipment that cannot be stowed below should be secured with the heaviest chain or wire cable practicable.  Pull up the boarding ladder, particularly on a catamaran or a monohull with a sugar scoop or boarding platform.
5.  Outboards are a major target: always lock them.  Lock dinghies to dock when ashore, using a long enough cable or chain so others can get their dinghies to the dock, too.  Hoist and chain the dinghy to the boat at night.  Chain the outboard separately to the rail or in the cockpit, or stow it below. Make your brand new clean shiny outboard less brand new clean and shiny, and therefore, less attractive.  Again, use good quality locks.
6.  Don't announce on the VHF that you are leaving the boat for a day of shopping or sightseeing or an evening out on the town.  If someone is calling a neighboring boat on the VHF, don't helpfully advise the caller that the neighbors are off the boat. If you call on the VHF for reservations at a restaurant or taxi, use your name, not your boat name.
7.  In high-risk areas, if asleep below during the day and especially at night, secure the companionway with barrel bolts and the hatches with screens or bars.  Use stainless steel hasps and fixings. Fix hinges internally so they cannot be pried off or unscrewed.
8.  Separate and hide valuables in multiple unpredictable areas onboard. In addition to hiding passports and boat papers, hide a copy of each in a different spot.  If possible, hide a spare GPS and handheld VHF radio.  Hide an extra set of passport photos with the passport copies to make it easier to get a replacement passport.  Hide a list of serial numbers for all equipment with the passport copies. When you purchase new equipment, register the purchase, along with the serial number, with the manufacturer: this is your proof of ownership, should the police ever request proof.
9.  Install and alarm system or use portable alarms to cover key access points.  A simple US$30 motion detector in the cockpit can do much to scare off thieves.  Be wary of using motion detectors like the car alarms, which can be set off at the least amount of motion; your neighbors will ignore the sound if there are too many false alarms.
10.  Have a response plan ready to use if boarded, whether at anchor or underway, with the emphasis on scaring away intruders.  For example, have an air horn, pepper spray, etc., next to your bunk.  If you have pepper spray, learn how to use it. Stay out of sight when the boat is approached, speaking from the companionway rather than cockpit in questionable circumstances.
11.  If you hear someone in the cockpit or on deck, DO NOT turn on any lights below - the light makes it possible for the intruders to see you.  Keep a flashlight next to your bunk for light. Turn on the spreader lights and any other exterior lights.
12.  Do not unlock a hatch or companionway to set off an alarm.  Install additional switches to set off the alarm from the cabins.
13.  When going ashore, store valuables in a pouch that can be tucked inside clothes rather than in a wallet, purse, fanny pack or daypack. Do not carry your wallet in a daypack or backpack; a clever pickpocket can get a wallet from a pack without you feeling anything.
14.  Carry only the amount of money needed for the day; a sacrificial stash in a pocket can be helpful.
15.  Be aware of your environment and dress/act accordingly.  Avoid wearing flashy clothing and expensive looking jewelry.
16.  Use a taxi if transiting high-risk neighborhoods; use a bus only if you are knowledgeable about the location of your destination and use of the bus system, i.e. how to identify that a bus is going in the proper direction.
17.  If you are involved in an incident, report it to the local authorities (police, marina management, tourist office, yachting and marine trade organization) and to the Caribbean Safety and Security Net.  An incident unreported, for all practical purposes, never happened.
18.  Don't discuss your departure plans (time and destination) with strangers on shore.  Don't describe your boat to strangers:  location, name, number of people on board, whether you are armed.
19.  Make two copies of the contents of your wallet:  credit cards (both sides), licenses, etc.  Send one copy to a contact at home and hide one copy along with your passport copy.  Be sure to have telephone numbers for the credit card companies to report a loss from abroad: usually the tool-free numbers they provide will not work from outside your home country.
20.   Many thefts occur while the boat is on the hard.  Don't forget about normal precautions when it is out of the water.
21.  If you call another boat on the VHF and they donít answer, donít keep calling.  They may be involved in a project and not be able to answer, or they may have the radio turned down or turned off, or they may be off the boat (you could be alerting someone listening in that they are off the boat).
22.  Do not let your credit cards out of your sight.  If a clerk in a store must take your card away from the counter to run it, go with the clerk.  Do not give anyone the opportunity to copy or clone your credit card information.  Check your credit card statements online occasionally to make sure that you are not the victim of credit card fraud, and if you find dubious charges, call the credit card company immediately.
23.  USUALLY, simply the presence of a dog on a boat is sufficient deterrent to boarders. However, if the dog barks at every passing dinghy and pirogue, it becomes like that motion detector in #9 and your neighbors will tend to ignore the dog.  On the other hand, if your dog has a different bark for friends than for strangers, that warning bark is your alarm, although your neighbors are not likely to hear the difference.

These precautions are not very different from the way you take care of your house or your car:  you lock your house when you are away and you lock your car when you leave it in a car park.  Your yacht is your house.