I second the recommendation for Beads of Paradise - it's the only dedicated bead stone I've found in the city with a good selection of antique beads.

But also stop by the 25th St Flea Market on Saturday or Sunday. There are usually several sellers with interesting selections of antique or even ancient beads from all over the world. Get there before noon for the best selection.
https://www.nycgo.com/shopping/west-25th-street-flea-market