Initial planning 3-4 weeks

Forgot to include Peleponnese with maybe Nafplion as a base.

We did a similar trip but also stayed on Paros. Don’t give Santorini more than two nights.
Napflio is a wonderful base. We also drove to Mystras, Olympia and Delphi.
We spent two weeks in Western Crete, a wonderful place to explore. We based in Chania with a trip to south coast Loutro as well.
We have already returned to Greece and plan to visit again.

We were in Greece in April 2018 for almost two weeks, then Crete by itself for 2 weeks in Sept 2019. Had a rental car both times, although not in Athens.

We arrived in Athens at night on the first trip, got some sleep for 1 night in a hotel, then immediately headed for the island Hydra, followed by picking up our car back on the mainland and touring the Peloponnese. We were there for 2 Easters - Western, and then Orthodox a week later. I see that April 2022 will have those Easters the 3rd and 4th Sundays. From Nafplio, include Nemea, in addition to Mycenae and Epidavros. Circling the clockwise and including the Mani Peninsula on the Peloponnese Peninsula, we toured Olympia before driving back to see Delphi (stay in Galaxidi), then Athens at the end, where the dar was turned in.

For Crete, we flew into Iraklio, stayed a 3 nights, then drove clockwise again, finishing in Hania. Lots of Minoan ruins sites for walking and exploring. Stay in the Lasithi Plateau (we chose Tzermiado) and hiking opportunities abound in the mountains surrounding the plateau. Gorge hiking on Crete is also popular, with several opportunities. Most people start at the top, and hike down the gorge, often ending at the ocean. We did the Gorge of the Dead (in ancient times, caves in the gorge walls were used as tombs) while staying in Kato Zakros, and the renowned Samaria Gorge. It’s only accessible in less-rainy months, and should be open by May, but possibly some time in April.

We went to Greece in 2018 and have a return trip planned for 2022.

2018-Santorini 3 nights, Naxos, 4 nights, Nafplio 4 nights, and Athens 3 nights.

2022-Crete 11 nights, Delphi 1 night, Meteora 2 nights,

One advice we got was to save Athens for last and fly to your furthest destination (which would be Crete for you). You have to fly out of Athens and the airport is about an hour away no reason to do it twice. It also is nice to adjust to being in Greece on an island.

Crete is very large and we are confining ourselves to Western part. Even then we have added one day to our trip. If you have more limited time, Chania is charming and well located for day trips. We are planning to hike the Samaria Gorge from the bottom (part way) instead of the usual way from the top. My husband's knees can't take the steep decent but also this way we will be able to hike without the usual crowds. It might be something to look into.

The most beautiful hike we have ever done is from Oia to Fira on Santorini. We stayed in Oia so started there (most start in Fira) and took the bus back. If you like hiking, I would suggest 3 nights for Santorini so you have time to do it and do some other site seeing. We rented a car for one day.

Nafplio is lovely and well located for day trips. We flew back to Athens airport from Naxos and rented a car to drive to Nafplio and returned the car before going into Athens.

I agree with the recommendation to do Athens last. It's a safety measure too: Domestic flights or ferry schedules can get messed up due to weather conditions any time of year, so it's always advisable to be somewhere near the airport at least a day early.

April can still be somewhat cool or windy, so it's smart to choose islands that are a bit farther south. Crete sounds like a good idea. Island hopping on the Cyclades would also be something you could comfortably do in 3 weeks.

Opinions on how much time to spend on Santorini differ, as you can read in this thread. If you have the slightest interest in archaeology, there is lots to see on Santorini besides the spectacular caldera. The hike along the caldera rim is also fantastic. My personal stance on this is that you are not doing Santorini justice if you just peek over the caldera rim, do the sunset shot at Oia, and move on. But to each their own.

Anyway, you could basically just hop on the ferry in Santorini after a couple of days and go north and spend time on one or two of the other Cyclades islands.

We spent 3 nights on Santorini (cave house in Oia) and rented a car so we had a chance to explore the island. Could have used a 4th night.

For advice on Crete buy Lonely Planet’s Crete 7th edition guidebook: https://shop.lonelyplanet.com/products/crete-7?via=Z2lkOi8vbG9uZWx5LXBsYW5ldC9Xb3JrYXJlYTo6Q2F0YWxvZzo6Q2F0ZWdvcnkvNTllZTQ5YmFmOTJlYTE0MTg2MDU4NWQ0.