First, make sure you really need to replace the bunks. I had a guy at a Nautique dealer tell me that I had better replace the bunks on 18-year-old trailer because they looked very rotted. So I went and replaced them. Well, it turned out these original cypress bunks were solid as can be. They just looked kind of funky on the bottoms where rusty staples had been removed when they were recarpeted several times. I wonder if my new much softer chemically-treated spruce bunks will last another 18 years.
Anyway, if you must replace the bunks, you could use cypress. If you want something cheaper and more readily available, you could do what I did and just get some ACQ pressure treated lumber and apply a couple of extra coats of preservative for good measure (I used Woodlife Coppercoat, available at my local building supply store). I felt that the extra perservative was necessary because my bunks required a bevel to be cut along the length, exposing the untreated (or less treated) core of the lumber. It's also always a good idea to treat the cut ends of pressure treated wood.
Also, as other have said, just be sure to use stainless hardware (bolts or lag screws) and the monel staples (might have to go to Boater's World or a similar store to get these--Home Depot, Lowes, and West Marine didn't have them).