At Minnie's you can expect Minnie and then frequently one or more Pooh characters. For our last visit we had: Minnie, Pooh, Tigger, Fairy Godmother, Chip and Captain Hook.
At Goofy's you will always see: Goofy, Pluto (Pluto is in front for photos but doesn't circulate. You can take your own photo with him or have them take one with a cute background for a cost). Last time we also saw:
Chip, Dale, Minnie, Snow White, Aurora, Peter Pan and Wendy.
I like both of these for characters because they both have a wide variety of characters that appeal to my girl and boy. I have never seen pooh characters at Goofy's however.
For food, Goofy's has a wider variety. Goofy's is a larger setting so the buffet is larger. At breakfast you will have a carved meat and things like breakfast enchiladas, pizza and chicken nuggets. You will also have a full dessert buffet at breakfast. Its more of a brunch. Minnie's is a breakfast with fewer selections but still plenty to choose from. I haven't gone hungry there for sure!
I prefer Goofy's for food, character wise they are about even. My experiences at Minnie's have generally been hectic but the convenience of being in the park is very nice. I do have to say, I wish Minnies would seat before park opening like the WDW park character breakfasts do. I always hate to waste the early hours of the park eating. At Goofy's you can book as early as 7:00 a.m. and unless its a very Early Entry day, be inside the park for opening or shortly thereafter. They also serve brunch much later, Minnie's generally stops by 11:00 or 11:30 so that the Plaza (the location of Minnie's) can revert back to a counter service lunch location. Goofy's definitely has longer hours and a more varied buffet. And Goofy's serves dinner as well so if breakfast isn't your thing then you always have the option to eat dinner there.
You cannot really go wrong with either!