A couple of thoughts come to mind. First is, you may be able to dye beads you already have to get your custom colors. I've used RIT dye to dye soft plastics. Plastic doesn't "take" the dye immediately, takes a little soak time, but it does work. This type of dye will bleed so keep whatever you create away from other plastics that you don't want to discolor.
Second thought is you could make a simple mold using RTV silicone caulk and then pour either an epoxy or clear casting compound colored with your desired tint. There's a post in the soft plastics forum about making a mold with RTV silicone. Basically you just need to get a tube of 100% silicone caulk (the kind that smells of vinegar). This is a moisture cure silicone. In a thickness for a mold it would take a long time to set up solid if more than about 1/4 inch thick, but since it is moisture cure, you can cause it to cure pretty fast (15 min?) by mixing in a few drops of water to act as the catalyst rather than wait for water from the air to be absorbed and cause it to cure. I've tried this and it does work. I would form a bead out of modeling clay (easy), coat it with paint or floor wax to get it shiny, and use that clay "bead" as the model for the mold. I've used the clear "future" floor wax to coat clay models and it works great. Just apply in thin coats and let each coat dry before next coat if a next coat is needed. You'd have to either make sure to incorporate a hole or just drill each bead. Whatever you do, don't use a glass "marble" as a model, RTV silicone sticks really tight to glass! For colorant, try something dry or oil based. Maybe scrape color from colored pastel pencils? or you could just use fine glitter in different colors. Since this is a small item you could use a thin epoxy for the plastic. One I like is a finish cure epoxy I get from a local hobby shop. If you want to keep your mold simple, just make it a 1-piece mold with a small flat spot where plastic is poured in and "Plaster of Paris" your pieces out when cured. A two-piece mold will require a release agent between the two halves. In that case I'd start with petroleum jelly for the release agent first. Also, if you do a two-piece mold I'd make it a "squish mold" rather than one that you pour for these really small parts.