Are there FDA restrictions on pigments used in waterproof eyeliner?

Yes. Under 21 CFR Parts 73, 74, and 82, only specific colorants are approved for eye-area use. Many cosmetic-grade lakes approved for general use are prohibited near the eyes. Your cosmetic chemist must cross-reference every colorant against the FDA's permitted list and, for EU markets, Annex IV of Regulation 1223/2009. AJ Cosmo Labs formulators are expected to demonstrate this regulatory fluency.