Carol RX has many locations, and they seem to have the best prices. They seem to have a pharmacy every 8 blocks in Santo Domingo. On Avenida Independencia, between Clinica Abreu and El Conde, there is also Farmacia San Judas Tadeo which isn't bad either, and has a big inventory.
I would also recommend avoiding Farmax - low inventories and high prices since they bought out Farmacia Vivian.