So are we talking just Greek myth or any in general? Your example implies the former, in which Ekhidna [Echidna] was an immortal monster, not a goddess, and also the mother/ancestor of almost half the other monsters in the mythology. Ekhidna's mother was a goddess, though, and her great-great-grandmother Keto [Ceto] was both a monster and a goddess (of the Sea). Keto didn't rule over any monsters, but the three Gorgons and the Hydra were her daughters. The Harpies were her nieces, being the daughters of her brother the sea-god Thaümas.
Skylla [Scylla], whom eirine has mentioned, was her stepdaughter, niece and great-niece all the same time. Skylla was originally a sea-nymph, but Kharybdis [Charybdis], a daughter of Poseidon and Gaia, was originally a giantess. Ladon, the hundred-headed dragon of the Hesperides, as well as the sleepless hundred-headed dragon of King Aietes in Colchis, were also supposed to have been Keto's sons. The three Seirenes [Sirens], who were a sort of breed of monster sea-nymph, are sometimes called daughters of Keto.
In terms of ruling over monsters, Hera seems to come close, since she used to collect and raise monsters from the time of the birth of her stepson Herakles [Hercules] in order that when he grew up they might become trials for him which might possibly kill him. These include the Hydra, the Nemean Lion (a son of Ekhidna), and the tribe of six-winged giants called the Gegeneēs, "Earth-Born," who lived on Arktonnesos. During Herakles' fight against the Hydra, Hera actually sent the Hydra some back-up, in the form the water-dragon's own friend Karkinos, a gigantic monster crab which lived with the Hydra in Lake Lerna. Karkinos clipped one of Herakles' toes off and the hero bashed it to death with his club. After the death of both monsters, Hera placed them in the Sky as the constellations Hydra ("Water-Snake") and Karkinon (Cancer, the "Crab").
Several of the monsters which were killed by heroes in Greek mythology were sent to ravage certain towns and cities by goddesses. The Sphinx was raised in the remotest parts of Aithiopia [Ethiopia] by the nine Muses, who taught the creature its infamous riddle, and it was sent to Thebes by Hera or Apollon [Apollo]. The Nemean Lion, another project of Hera's, was suckled from in its infancy by the moon-goddess Selene. The monstrous Teumessian Fox was sent to Thebes by Themis. The monstrous Kalydonian Boar was sent to Aitolia by Artemis.
The only other notable encounters between goddesses and monsters in the mythology that I can think of are: that all the Olympian goddesses fought against the Giants when they attacked the town of the gods during the conflict that came to be known as the Giants' War; and that an Oceanid named Kallirrhœ married the sea-monster Khrysaor (son of Medusa) and by him became the mother of Ekhidna and of the ogre Geryones.