Plane board sides evenly before joining
What you are wanting to do would be better on a tablesaw because of the amount of material to remove.  A Jointer or Planer is good for making very strait edges and tight joints, but with 1/2" of variation, you're not to that point yet.

What you want to do is a form of a "tapering cut" on a table saw, but instead of tapering, you just want to make the edge straight.  Tapering is when you have a board that is 6' long, and the top needs to be 3" wide and the bottom needs to be 4" to make up for a crooked wall or similar.

http://www.finehomebuilding.com/2014/09/25/how-to-cut-a-tapered-board-on-a-tablesaw

There are many videos and how to's if you search for making a tapered cut, and they usually involve attaching your board to a straight board at an angle.  You'll do the same thing, but without the angle.

I've done this with boards as long as 8' and a taper of 1/2" or so relatively easily.