I'm late to the party...
Echoing the pet and crafts shops- they'll have glass, ceramic, plastic and wooden ones for things like dioramas, dollhouses, aquarium/terrariums and knick-knacks in general- and adding mega-gardening shops as well. Places like Garden Ridge should have all kinds of little pottery pieces used for decor or spice pots.
Also check out Pier One and The Container Store- they have tiny glass and plastic bottles with lids or stoppers.