Extremely safe. My daughter-in-law was so concerned just like you are. She was sending her one and only child away for two hours on a boat! First of all, you have to sign the kids in. You will be given a permission slip for each one of the kids. You will also have an opportunity at that time to give any food allergies they might have (my granddaughter develops a rash with anything red berryish). You will also be given a receipt and a beeper. You have to have BOTH to get your kids back. After that, you will get your kids fitted with life jackets (provided). You pick the ones but a Cast Member will check the fit before anyone boards the boat. Each of the kids will get a pirate bandana with Mickey ears and their name on one of the ears. That way, the Cast Members can call each child by their name.
The kids are paired up. Not sure what they would do with your four but they will board and disembark in a pair. At 9:20 or so, the kids are gathered together and given their "instructions". That's when they are paired up. My granddaughter was solo and she was put with another six year old girl. They were best friends by the time that cruise ended.
At 9:25, the kids board the boat, two by two. You can see the entire thing from the dock. It's very open and very well organized. There are tons of photo ops. At exactly 9:30, the boat (which is a pontoon boat with a Jolly Roger in the back) pulls away.
After all this - my daughter-in-law turned to me and said "leave it to Disney to make this so easy".
When the boat gets back (at exactly 11:30), you definitely have to show your receipt and your beeper. The kids won't get off that boat without both.
Hints - get there when the marina opens up at 9:00. After your pirates are properly outfitted, you will have a great time taking pictures at the one end of the dock with the castle in the background. And make sure they go to the bathroom before you get there. Can you imagine kids for two hours and a full bladder?
This is so safe, you shouldn't worry about it all.