Knossos is good, of course - but you'll be swimming in gap-year students and American OAPS
Far better nowadays is the remarkable "Palace of Malia", an only slightly smaller palace currently under summer excavation on the eastern side of the town of Malia, just follow the signs. Much more fun to see a "live" site at work, and it'll be by no means as crowded.
There's also a dedicated war museum in the village of Episkopi, seven miles inland from Heraklion, with an associated vehicle park in the country behind the town. However, this is a "seasonal" museum, owned by a guy from Athens who only comes across for the summer season.
One of the most suprising sites to visit on the island is the Lassithi Plateau; follow signs from Stalis. The most amazing piece of switchback road takes you up into the mountains, eventually debouching into the "plateau" - which is actually a bowl-shaped fertile valley once famous for its carpeting of farmers' windmills. It's once of the most beautiful places on earth, and you may as well be stepping back 60 years in time. AND it was Paddy Fermor's stamping ground for half his time on the island
