Top islands for hiking according to Lonely Planet 

Crete: Samaria Gorge is one of Europe’s most popular hikes, with myriad wildflowers and endangered wildlife. The Zakros and Kato Zakros trail through the mysterious Valley of the Dead leads to a remote Minoan palace site.
Andros: Well-established hiking paths connect villages or trace unspoilt valleys marked by ancient water mills.
Naxos: The broad central plain of olive groves, Tragaea has plenty of trails linking rural villages. Filoti offers a strenuous climb to the Cave of Zeus, a natural cavern on the slopes of Mt Zeus.
Tilos: Countless traditional trails follow dramatic clifftops and lead down to isolated beaches; it’s also a bird-lover’s paradise.
Nisyros: This lush volcanic island offers hikes that lead into the hissing craters of Mt Polyvotis.
Paxi: A diminutive Ionian isle perfect for escaping the crowds on paths along ancient olive groves and snaking dry-stone walls.
Ithaki: Mythology fans can hike between sites linked to the Trojan War hero Odysseus.
Samos: The quiet interior of this Aegean island hides mountain villages and forested slopes of Mt Ambelos.
Hydra: A vehicle-free island in the Saronic Gulf with well-maintained paths to beaches and monasteries.
Alonnisos: A network of established, easy trails leads to pristine beaches.