It sounds like you have a great trip planned, with enough time to see most of the cities! And April and May are great times to travel since the weather is getting quite nice in most places.
For your Milan/Cinque Terre dilemma, I did both and I think they are both amazing places to go. If you want to do some hiking at all during your adventures, I would suggest Cinque Terre. But at the same time, things are not open as late there. It's got a cozy village feel, but the food/drink are exceptional. When I went I remember it was difficult to find hostels actually located in one of the 5 villages, and the one we did get to had a curfew. But it was totally worth it for the views, and finding isolated swimming spots (at the same time, there are crazy ridiculous tourist beaches which I suggest you avoid at all costs. It is a nice place if you want to stop looking a Cathedrals and museums; instead you will enjoy lovely terraced vineyards and little towns along rocky cliffs, with very nice natural beauty. Milan: good for history, but overpriced and filled with tourists. Check out the weather averages for Cinque Terre before you decide to go though, cause lots of rain would not be fun for small, disconnected villages