In short
Easy and frequent. Chania ↔ Rethymno ~1h (€6.20-7.80), Rethymno ↔ Heraklion ~1h30 (~€9), roughly hourly. Chania ↔ Heraklion: 3h by omnibus (€15-16) or exactly 2h with the EXPRESS (4/day: 09:30, 12:30, 15:30, 18:30, non-stop). The EXPRESS skips Rethymno.