I too have a black lund, I wouldnt use CLR on it, that us corrosive and may damage the paint. Treat it like your car/truck - its just paint on metal, same as the car. For water spots, use a cleaner wax, lots of good suggestions here - Meguiars and Mothers are 2 good brands that are easily bought here. Keep it waxed and the water spots wont stay.
Also, if you trailer, keep a couple of the microfibre drying towels in the boat and dry it off when you pull it out of the water - will help to keep it clean and help with not transporting invasive species.
Andrew