This has been discussed quite often on the site (try the Search feature) but you are pretty much limited to the following:
1. ASM (
www.pokerchips.com) - Most popular custom clay chips because of price. You can choose from several different molds, different colors (body & edgespot) and with or without inlays. The downsides are long wait times (2-3 months I believe) and limited options for edgespots (they only do 3 1" single color edgespots).
2. TR King (
www.trking.com) - Much more flexible than ASM but more expensive. The price varies depending on Dennis's mood (he's the GM) , options and the quantity. Typically, quotes seem to vary from 1.75/chip for 500 chips to .85/chip for 5000 chips. They offer the most options for edgespot combinations and top quality chips (10 grams).
3. Paulson - Not much to talk about here since they don't offer any custom edgespot combinations (stock colors) and require a minimum order of 100,000 chips for a custom inlay.
4. Blue Chip - Don't know much about them but some folks have dealt directly with them (Samurai Group buy) and other have relationships with them that allow custom orders (Nevada Jacks but I don't believe they advertise that fact).
Good luck.