I was at Disney in June 2010 from June 4th to June 16th. I don't know if it was because it was almost 3 years ago, but I actually thought it was just as crowded as when I went this past year in late October.
It really wasn't that bad, IMO. The only thing that I didn't like was that it was HOT. I tried going to Downtown Disney one morning and almost died. It wasn't so much that I was feeling hot and sweaty (because I wasn't even sweating) as the actual feeling of the sun burning my skin, it felt like I was walking on the surface of the sun.
But other than that, if I had to choose between the 2 months I would pick June. I thought it was much better to just be able to wear shorts everyday and never worry about bringing a coat.
Even though I hate hot weather, at Disney I feel it's best because I dislike having to bring extra clothes to the park and keep taking off coats, putting back on, never knowing what the weather is going to be like. I had no idea it could be like that in October, I figured it would be hot enough for water parks every day, just not horribly hot like the summer. But I was wrong...most days I was cold and it didn't help that the the air conditioning is kept on in most stores and rides even when it's very cold.
So unlike in the summer, when you can go to a ride or store to cool down, there's no where to go to warm up when it's unseasonally cold.
Also, in June, since the parks were open until 1am, 3am a lot of days (EMH) I could go back to the hotel and take a nap on the hours when it was really hot. It really wasn't too bad before 11am or so and after 3-4pm. That way I was at the parks when the weather was nice and it wasn't very crowded.