I know a lot of folks have had great experiences with MJT/USACG and Musikraft. I haven't bought any of their necks so can't comment there, but have been very happy with Allparts and Warmoth.
Allparts isn't really "custom" but they make a decent array of necks as long as you're not looking for any exotic woods. They are made in Japan, so when it comes to AmStrat replacement necks, the heel to pocket fit may be a bit snug (to the point of cracking your finish) just due to the metric to imperial interface.
I just got a Warmoth neck for another partcaster I've got going. The Warmoth neck is really nice, but I would say there are some design variations from a true Fender, mainly at the neck-to-headstock transition. You wouldn't notice anything looking at it from the front, but you'll notice it on the back. It has no negative functional impact... but if you're looking for an exact Fender neck repro, Warmoth wouldn't be it.