New Delhi and Mumbai has various daily flights for Athens. Qatar Airways, Jet Airways, Emirates, Etihad, Egypt Air, Turkish Airlines offer services to Athens. From there, you can take summer charter flights to Crete.
You can fly to Athens and from there you can take summer charter flights to Crete which will land you in the city of Heraklion.
To reach Crete by boat, you can board it from Athens which will drop you on one of the 6 ports located at Heraklion, Chania, Rethymno, Ag. Nikolas, Sitia, and Kastelli-Kissamou. Crete connects through these ports with Piraeus, Santorini, Sikinos and more ports around Athens.