Sounds like it would be good for me to share the results of my research.
Prawn Designs - The cheapest laser engraver that I've found for small orders, however he's a one man shop so I don't know how long orders will take.
Custom Dice - They'll customize any type of dice as far as I can tell with multiple sizes, however I got quoted a minimum order of $50.
Chessex - They will only customize d6s, minimum order is 10, price is per side customized.
Q-Workshop - Will customize any kind of dice but their minimum order is 50 pieces, also they're located in the UK so shipping can be expensive.
Crystal Caste - If you want a lot of d6s from an established company this is a good way to go, minimum order is 25.
Dice and Games Ltd - If you're in the UK they'll laser cut dice for you, minimum order is 25.
Those are the only places that I could find that were anywhere near reasonable.