I used untreated 2X4s 10' long for my 16' jon. I coated them with wood preservative on both sides and the ends - two coats - then I bought PVC fence post covers from Lowe's HIW, ripped them lengthwise and then screwed them to the sides of the lumber. The covers are meant to go over a 4X4 post and are only 8' long so I got 3 and patched them in so they covered the whole bunk. The absolute best trailer I ever used. The only thing I had to remember was to not unhook the winch hook until the transom of the boat was in the water. Otherwise it would slide off the trailer onto the ramp. I then could power load the boat with the transom mounted trolling motor when I retrieved it.
If you used the bunk covers you could use any lumber you want as it will not contact the aluminum hull.
The second picture is how I screwed then in from the sides so the screws never touched the boat. And it shows how I bent down the PVC cover at the back end of the bunk.