Boat security?

It all depends on where you cruise. Cruising the eastern U.S., locking your doors is barely needed. Depending on the area I may use the deck alarm when at dock, but not on the hook. Off the coast of Somalia there'd be no stopping. In any questionable location a deck alarm would be a minimum. Better to post a watch so as to know of potential trouble before it's on board. Same goes for distress signals. On the eastern U.S., always render assistance. In questionable areas or situations relay messages to the authorities and stand off at a safe distance. Anybody brought on board must be scrutinized for weapons as they are boarding. Never put your vessel at risk.
I always have a knife close at hand, but mostly for in case of accident (such as a line wraping around a limb). Mace & pepper spray are acceptable in most places. Many jurisdictions prohibit firearms and stun guns and having them may get you in more trouble than they'll save you from. If you carry lethal weapons be sure to check the regs in the areas you're cruising, and never pull a weapon unless you will immediately use it. It may well be taken away and used on you.

Keeping a radar alarm set while you are anchored will alert you to any boats in your vicinity before they come alongside. Keep all of the doors locked. I have not seen a deck alarm installed on any yachts but it easily could be done with a motion sensing device or several.

Motion sensors don't work too well on most boats; too much moving about. The alarms I've seen are the beam type, generally installed on steps and at cabin entrances but can be placed anywhere. I don't recommend the magnetic type as they are too easy to spot and thwart, plus, by the time it sounds the intruder is already in. Best bet though, if you have doubts about a place don't be there or post a watch. There are also computer monitoring programs for when you're away such as Sea Key (I believe) that will track a stolen boat like Lojack or Northstar for cars.
There are also cheap local (battery operated) alarms that can be placed on doors or under a mat, but I wouldn't recommend them. As a temporary measure you can also "string" you deck using fishing line to trip an intruder.
The radar alarm will not offer much protection. It will not detect a swimmer and most likely not detect a small inflatable unless the sensitivity is set to also alert when a bird passes.

Google: Gun laws in....
Then contact the local customs office.

That's like walking up to a cop with crack in your hand saying you found this. You're in possession. In NYC I believe that's an automatic year on Riker's Island.
"New York’s gun and weapon crimes are among the Nation’s toughest. Most gun crimes, even the simple possession of concealed handgun, carry jail time. Even in situations where you defend yourself, you may be charged with possession of a firearm if you have no license to carry that weapon."
BTW, "Socialist Republic"? Please! Take a walk through Tiananmen Square with a gun in your hand some time and draw that comparison.

Yes if it's an assault weapon. Otherwise contact the NYPD in advance for a permit. That's why I suggested earlier "Google: Gun laws in....". NYC is considered a hightened security area. It has nothing to do with Socialism or libralism. We are a major target for both gang and terrorist activity. Security and protecting the population is not taken casually.
You have to ask the right question of the right people in the right place. The CG doesn't interpret the local laws, just enforce. Guns are considered very serious business everywhere, even in Florida (try driving through Miami with a gun visable in your car sometime. Not recommended.). BTW, I assume that captain is no longer a captain or at least he will no longer be when his case is finished. The year in jail is only the tip of the iceberg he's facing (fines, community service, lawyers, revocation of his Master's license, he could even find himself on a no-fly list).

Was it the owner's wish to have a firearm aboard? I have seen no answer to that question(or if it is even relevant). Pity the captain will take the heat if that is the case.

Can you get away with this anywhere? Maybe Texas, where not everyone has a stick up their $#@.

Well said.

Completely irrelevent. I used to tell my mom that the smokes I was carrying belonged to a friend. Just about everyone caught with drugs says they belong to someone else. The results are the same (although I'd rather get caught by the cops than my mom. ) Possession is 9/10 of the law.
P.S. I think Texas executes more people than any other state with the possible exception of Louisiana. So I be careful about using a gun there as well.

That's life when traveling with guns.
About getting busted by NY cops in NJ, that's unlikely (but possible). It may have been NY/NJ Port Authority cops. BTW, if the case was an innocent transgression or the owner accepts responsibility the worst case scenario probably won't come about, but it won't be fun or cheap for anyone involved.

Baring PMS your marriage is only dangerous to you. Plus, if everyone had the option not to renew when they moved to another state, well... There are places where $5.00 gets you a carry permit for a full auto with no background check. Thankfully that's not the standard in NY. That's why it doesn't cross state, county, city or country lines. In NY and many other place there is one standard for an open carry permit, another for concealed, another for home protection, another for assault weapons, automatics and machine guns, etc.. still another for hunting rifles. Most places in this country have the most relaxed standards for (unaltered) shotguns. When it comes to something as dangerous as a gun I'd hate to have people coming to my door carrying because they were authorized to have a gun by Georgia or Texas. There probably would be a national standard, but the NRA has a very powerful lobby.
BTW, in NY it is also illegal to have a stun gun; pepper spray cannot be bought by mail order and the owner must register.

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The reason crime is lower in the US then other countries it's because they know private citizens MAY be armed and they are facing that risk when breaking into someone's home or robbing someone.

When the UK took away the guns, homicide went up 48% and home invasions went up 52% and have stayed there. WHY, because criminals can always get guns, but when they know the good citizens can't they have nothing to fear.

There are PLENTY of criminals walking around NY right this minute with illegal guns, rest assured that someone authorized to carry a gun and has passed FBI background checks is 99.9% of the time not going to be knocking on your door with harm in mind.

This is not true anywhere in the US. You are joking, right?

You evidently don't know much about firearm laws. Most of this is totally inaccurate or simply not true.