FWIW
I had the 5.5's on my 4runner last year and they didn'y settle that much. I removed a leaf and it dropped it almost an inch. With a 1.5" lift shackle I cleared 37's. I did trim out some rust I had in the rear fenders though.
I now have 4"ers on the rear of the same rig (only it's a truck with a "custom" bed on the back) and they seem to be about the same height really. I have all the leafs in them still and the rig is lighter in the rear than it was when it was the 4runner.
I was going to get 3's but it would have made my ass lower than the front (44044's) and I like the way my front works as is.
That being said, do YOU plan to run with the top on all the time? Do you haul a lot of gear? If so, go with the 5.5' rears
If you travel fairly light, the 4's will do fine.
If you travel real light and bob the rear and didtch the top, get the 3's and work with the front to get it where it needs to be.
I voted for the 4's though.