Monel staples are easier to find than stainless, West Marine or Boater's work has them. They are a high nickel alloy that is even better than stainless in that it is not as brittle, which is better for staples.
I have found that a better grade of indoor/outdoor carpet holds up much longer than the bunk carpeting that comes standard. I have also found aluminum nails very good for attaching carpet to bunk boards. Last time I bought aluminum nails they were too long so I just trimmed to length I needed with side cutter pliers.