Both make very high quality stuff. I agree completely with previous posts - Musikraft is the only game if you need a 2-1/4" Neck Pocket. Also, Musikraft offers a true 'Dinky' body - which isn't quite the same as Warmoth's 'Soloist' offering. I am partial to the true 'Charvel' shape rear control cavity that Musikraft offers as opposed to the big 'Kidney' rear control cavity on Warmoth bodies. Musikraft also offers Northern Hard Ash which Warmoth does not.
That said, I do have 3 Warmoth builds that are just really sensational guitars. I love the Contoured Heel and the '.720 Mod' that Warmoth offers - which drops the neck deeper into the neck pocket. Can't go wrong with either offering - kind of boils down to which body wood you need and which options you prefer.