I believe I have found several places in The Lives of Eminent Philosophers, Book X where atoms are referred to something other than ἄτομος (and declensions thereof). Here are those found in Ep. Her. and Pyth.:
ATOMA — “elements” (Bailey), “particles” (Munro)
ATOMOI — “atoms” (Bailey)
ATOMOIΣ — “atoms” (Bailey)
ATOMOΣ — “atom” (Bailey)
ATOMOYΣ — “first beginnings”, “atoms” (Bailey)
ATOMΩMON — “atoms” (Bailey)
ATOMΩN — “atoms” (Bailey)
ATOMῼ — “atom” (Bailey)
Here are additional words (I believe) used in extant texts to refer to the eternal, indivisible particles, namely, declensions of μέρος (méros or "parts"), ὄγκος (ónkos or "mass"), and λεπτός (leptós or "minute").
ΛEΠTOMEPHΣ — “fine particles” (Hicks)
ΣXHMATIΣMOΣ — “atoms” (Hicks)
ΣXHMATIΣMOY — “atoms” (Hicks)
MEPIΣIN — “certain particles” (Hicks)
OMOYPHΣIN — “certain particles” (Hicks)
OΓKOI — “particles” (Hicks)
OΓKOYΣ — “atoms” or “parts” (Hicks)
OΓKΩN — “particles” (Hicks)
Have you come across any other words in ancient Greek that refer to "atoms"?