I have electric brakes on my equipment trailer and surge brakes on my boat trailer. I use both all the time and they both work just fine if you maintain them which poor maintenance is the reason either type can fail. The biggest old issue with surge was when you tried to back up an incline then the brakes would fight you. As I mentioned in my earlier post, there are new surge back backing plates and assemblies that do not engage when in reverse. The clunking you mentioned comes from the being worn out or out of fluid typically.
So, just to clarify on electric brakes. The wiring on electric brake assemblies goes into a sealed coil (note sealed coil and this is reqular wire that does not burn out like a light bulb) that creates a magnetic field to actuate the brakes. The area for concern is where you connect the wiring to the brake wires at the wheel. As someone mentioned above, use the connectors with the adhesive sealant inside them to make sure the water doesn't get to the bar wire, they won't short out but will corrode if water gets to them. If you go with electric brakes, make sure you run an extra ground wire in your wire harness for the trailer chassis (good idea even for your trailer lights) and don't rely upon a ground through the trailer hitch ball. In operation, you will set your brake controller with the boat on the trailer but remember once you unload your boat, you need to back off on the controller otherwise your tires will likely lock up when stopping with the trailer empty. Surge brakes engage at a rate due to the load so a light trailer without boat sets up less quickly and hard than when it is loaded.
Do I have a preference? Yes, electric brakes but being an electrical engineer, I prefer to minimize wires in water to avoid the inevitable corrosion that eventually seems to creep in.... Also, I can tow my boat with another vehicle without having to put a controller in the other vehicle although probably not legal to do that and I don't normally. So, one more thing, I believe most, if not all states, require all wheels on a trailer that touch the ground must have brakes on every wheel. Something to consider if you are doing a new set of brakes on multiple axle trailers.
