If you are travelling exclusively by public transport, I think Chania is a better choice: unlike in Heraklion, the airport bus takes you directly to Chania town station from where you can catch the bus to Rethymnon. Chania is also a quieter airport than Heraklion IMHO. However, I, personally, will continue to use Heraklion simply because I am very familiar with the set-up there, and find there is more variety in using that route.