Yes, "года через три" sounds perfect. "Через года три" can be heard in everyday speech occasionally, but it sounds clumsy, like a person changed his or her mind in the middle of a phrase. Usually prepositions and such are put between a numeral and a definitive word.
eg.
Лет с десяти я начал мечтать о кругосветном путешествии.
Я приду минут через двадцать.