i wish i knew... i always buy online...
the only store near me that i know of that sells indigo, sells it mixed with henna and metals and other impurities (compound henna/"black henna")... so if you buy locally, make sure you ask questions so you dont get something adulterated.
maybe they dont sell it in stores because it has a shorter shelf life than henna, and to keep it fresh would cost more time/energy/money than what it's worth since there isn't a huge demand for indigo in certain places... maybe you can ask them if they could order it to their store from their supplier for you... it may cut out the shipping that you would have paid online... hth