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Nobody could say a best place but I will tell you a GOOD place.
Samos, right over near Turkey. It has a beaut little harbour on the other side in the town of Pythagoreio. It is known as Pythagoras' island.
Get there from Athens by ferry (not me again) or plane. Google it up. Cheers.
Are you going to charter there? Where will be your base? How long have you got? What do you like, the sailing or the trips ashore? My wife and I spent a couple of seasons around the Ionian on Ivory Moon.
JR
Yes we chartering out of lefkas for 4weeks and not sure of the best way around as we been told about fish firms taking up a lot of the areas 
Its not the fish farms .. its the charter fleets! They do like to line up along the docks in the towns, so you need to get in early if you want a central spot, prolly before 4pm. If you are happy to anchor there are many spots, no one best place, its all great. The afternoon breeze comes in about 2pm, and can blow up to 20 knots before settling in the evening, can make going stern to a dock a bit tricky.
From Levkas you could go north to Preveza, Antipaxos, Paxos and Corfu. The Gulf of Amvrakikos behind Preveza has good sailing but yes there are fish farms there. Plenty of history too, Ceasar Augustus saw off Mark Antony and Cleopatra's fleet in this very place. Paxos is very beautiful, water great but very crowded.
Probably more likely you will go south. You could plan a clockwise circuit after you have visited Nydri south of Levkada. Check out the taverna up the hill behind Rabbit's boatyard in Vlyho Bay. No charterers, all locals. We had a favourite little bay on the NW corner of Meganisi, room for 2 boats, but many power boats in the weekends. Then towards the mainland you can anchor off the beach at Kamilavka. The east side of Kalamos Island has anchorages, but they are generally deep and there are fish farms in some. One House bay on Atokos Island is anchorable but boats make a beeline for it from early in the morning. We like the bay of Petalas, excellent shelter, warm water for swimming but not the clearest. Then around the corner into the Gulfs of Patras and Corinth, there is a marked anchorage on the south side of the island on the corner (I think its called Dragon Island can't check my book just now), but its very deep and has a fish farm now. Go up the canal to Mesolonghi, tie up anywhere on the dock or anchor, lots of retaurants on the waterfront. Find out where Keats' heart is buried.
Then a highlight is to make you way east in the Gulfs as far as Itea, where there is splendid free dockage and you can catch a bus to visit the Oracle at Delphi. Watch the weather in the Gulfs, you'll have a beat to Itea, or back. Stops on the way at Navpaktos, Trizona dock or anchor inside or out it, Galaxidhi dock. With time on your side you could go to Corinth, not much to see there but the Canal of course. Go back out the Gulfs, visit Zakinthos in the town, or anchor round the corner in Lagana.
From Zakinthos start back north, Sami on Kephalonia, Frikes further north but very very crowded, Vathy and the bay to the west on Ithaka, then back towards Meganisi and Levkas.
4 weeks is not enough! Maybe do some planning on these thoughts, and feel free to drop us a line if you want any more detail etc.
Best of luck! Ivory Moon and her crew envy you.
JR
Fish farms are not really much of a problem in the ionion (other parts of greece yes). There are many many anchorages in the ionion once you have mastered the long lines ashore technique. Make sure you do as it opens up little coves etc where you can be the only boat even in August when all around you is maddening crowds.
Free swinging anchorages are much rarer and usually full. June is a good time as its before the main crowds hit so most town quays usually have a spot for you as well. You will need to get the med mooring technique down pat or become the entertainment for the dock in cross winds 
The crowds in ionion are getting worse every year with around 40% more charter boats than 2 years ago now.
Ivory moons itinerary is a good one - south has more than north but its only a day from the lefkas canal to southern corfu so you can do both in 4 weeks easily. If you are over the crowds the gulf of patras is a good option. Some fantastic stops as far east as you care to go though usually around the galaxis bridge the prevailing winds change. We had a surreal day there where we were sailing west DDW under spinnaker while the boat approaching us was also DDW under spinnaker. It lasted till we were about 500 meters apart.
Personally I would let the weather determine the plan especially in June when the summer pattern is still not fully established. If the week you pick up the boat its northerlies go into the inland see south of lefkas. If its calms to westerlies or southerlies then head north to corfu till the pattern changes back to north then its a downwind sail back past lefkas. Too many charterers end up motoring everywhere and sailing little cos they have a limited time and a must do itinerary in their heads regardless of what the weather is doing.
