There's no differece between the two words. They are completely the same both in meaning and pronunciation. It's just the difference in transliteration.
There is a rule in JIS that the long vowel mark is not put at the end of a foreign word when the number of moras of the word is more than three. For instance, "car" is カー, "cover" is カバー, but "moter" is モータ, not モーター, since モータ is three moras. This rule is for industrial activities, so モーター is quite commonly used in other fields e.g. in literature or daily conversation. That's why those two different transliterations exist. (The rule is revised and it's acceptable to put or not to put the long vowel mark at the end of a word even in JIS now.)