We are interested in clean rocky places.
I am also hoping someone will give some advice on this.
If you snorkel to see fish, you need to swim from a beach that has a rocky bottom, and rock pools. I don't there is anywhere in the Rethymnon area that qualifies. There may be somewhere along that coast, and if there is I'm sure someone will tell you about it. But the south coast is better snorkelling territory.
In general I'm sure that the better snorkelling is going to be on the south coast, by some way. Much of the (kms long) beaches from Rethymnon are predominantly sandy. I wonder (and perhaps DE gerlion may know) if the rocky/pebbly beach of Gerani, several kms to the west of Rethymon, might have some better snorkelling that the sandier beaches if you want to try the north coast in that area (not to be confused of the small resort of Gerani west of Chania).