Good point Toxic. I was pondering that, with something bothering me about pressure treated. Then I remembered the last time I used pressure treated lumber and the warning I read on a label and heard from a store employee about using the right fasteners in it due to the chemicals. Not only might it react with a tin rig - it might also react with the metal trailer brackets and whatever fasteners you use to secure it. Pressure treated is more for keeping out termites and fungus, not waterproofing. I still had to put a stain / sealer on the pressure treated I used on my deck.
I'm a huge "do it yourself" kind of guy, but I also take into account that it may be more time consuming and expensive than buying replacements, and I take that into account. That being said, many manufacturers offer "treated" bunk boards, already assembled. Treated with what, I don't know. They don't say pressure treated, just treated. Looking at the price, taking into account that they already have the proper carpet on them, glued and stapled in place, etc... You might want to just buy them. Tie Down sells 3, 4, and 5 foot models, and I've found them as cheap as $21, $29, and $34 for pairs of each size. Check this link to see what I'm talking about:
http://www.wholesalemarine.com/p/T-D-86127/Replacement+Boat+Trailer+Bunk+Boards.html
I haven't replaced my own bunks, but I have done the fenderwells on a previous boat. I bought regular plywood of the same thickness as the originals. I used an outdoor paint on it, and put on several coats - ensuring I got the edges really good. When it was nice and sealed, I covered it with black indoor / outdoor carpeting I got from Lowes that matched the original. It's not the outdoor plastic feeling stuff - it feels like really short haired indoor carpet. I used the outdoor carpet glue they recommended - really strong stuff.
All the best,
Glenn