Turns out I just sewed a new shifter boot out of some black naugahyde I had lying around using what remained of the rubber one as a pattern. I cut the base of the rubber boot to hold the new one in place on the console like a rubber band.
I would have made a DIY out of it, but it isn't likely anyone else would be cheap enough (or handy enough with a sewing machine) to do that over the $30 or whatever it costs for a new rubber one
Actually looks pretty good though, you'd never know!