Man I removed mine and to be honest that cleaned up the rear end alot. Especially being lifted. If it doesn't match the tires you have on it now or plan to go with bigger tires in the future, then just remove it. Otherwise, check out Solid94 (Adam's) spare tire holder he made. Not my thing, but looks badass for what it is.
Only other option I've seen is the guys who run an actual roof rack and put the tire up in the middle of that but that ain't my thing either. Let us know what you do, but I'd just pull it out! If you do, be sure to tighten up the spare holder on the wire all the way up or else it will swing around down there and make all kind of racket.