Formal:
* Les grands esprits se rencontrent. (This is the most literal and formal translation.)
Informal:
* Les esprits forts se ressemblent. (This emphasizes the strength and similarity of the minds.)
* Les têtes bien faites se ressemblent. (This focuses on the intelligence and similarity of the minds.)
* Qui se ressemble s'assemble. (This is a proverb meaning "birds of a feather flock together", which can be used as a translation for "great minds think alike".)
The best translation for you will depend on the context and the tone you want to convey.