I'm not a Fringe fan, but I liked Noble's work on LotR and Transformers: Prime. I think he could do a very credible Thrawn, even if they just had him do the voice and they did motion-capture to make a CG face (to save him from hours of make-up time every day).
Hmm, perhaps... I dunno, I had Benedict Cumberbatch in mind for Thrawn. However, now that you mention him I think John would actually make an excellent C'Baoth. Not that he wouldn't make a good Thrawn too.