On the west of Chania there's 'Golden Beach', located at set of three small peninsulas. Lots of fish, lots of boulders, and shallowish, but also many people.
For Heraklion you will have to go to the south coast (Matala, Lentas, Tsoutsouros) as the Heraklion coast is one big sand bank, although towards Rethymno the north coast has some interesting spots.
Kali Limenes, in the south of the Heraklion province, has the shipwreck of the Byron 1 (renamed from Roybank) in shallow water. There's a dive center ("Sea Lovers") in the nearby village Platia Peramata that does scuba excursions to the wreck.
Just a bit past Retymno there's Gerani, and around the corner from there, direction Chania, it's great for snorkeling with interesting rock formations and a good diversity of fish, but be careful when there's northern wind.