I have to agree the discrepancy in sales is due in no small part to people wanting to buy American. The X is also slightly bigger and therefore has more people / cargo capacity than the 4Runner, which could also be a factor. I also think the Xs has a more refined / posh interior - cept for maybe the third gen 4Runners, which have traditionally been more spartan.
If buying American isn't a big factor for you, and if you're looking to build an off-road or even dual-purpose / weekend warrior vehicle, I'd personally go with the 4Runner. Wether we like it or not, the current fact is that the aftermarket embraces the 4Runner much moren than the X.
Hopefully this is slowly beginning to change as I am seeing more and more Xs in 4x4 / offroad mags, etc., but currently, unless you do your fab work or pay high dollars to have something custom made, you can't even get basic off road necessities like solid sliders, bumpers, whinch mounts, etc. for our Xs. There's only 1 company that makes a lift kit for the 96+s (Superlift), and since I have it, I can tell you that (1) it only allows for the minimal tire size you'd want for even moderate offroading, and (2) it's more cosmetic than functional since it doesn't increase ground clearance nor travel in the front.
Conversely, there are scores and scores of places that make all kinds of commercially avaialble, bolt-on-anything for the 4Runners that can more easily turn them into much more capable off-roaders, and probably for less dollars. Additionally, their smaller size makes them more trail friendly than our Xs - at least for the tight-woods trails of the NE. 4Runners are also supposedly extremely, extremely reliable and hold their value better than our Xs.
Now, don't everybody go getting' your panties in a bunch... I love my X and I bought it over a 4Runner -or anything else for that matter - because buying American matters to me and for my needs, I personally like the bigger size of the X better. Just keep hopin-n-hopin that the aftermarket catches on...
Good luck, I don't think you can wrong either way. Figure out which drives better and which better suits your needs - at least 80% of the time and go with that one.