Which would be my best choice for a 4 and 6 year old?
First of all, here is the link to our character meal photo & information thread, which may help you decide:
http://www.disboards.com/showthread.php?t=2234435
Do the 4-year-old and 6-year-old prefer any certain characters? Are Goofy's Kitchen and Minnie & Friends the only choices or would you be interested in doing the Surf's Up with Mickey meal as well (that is the only meal with Mickey)?
Minnie & Friends has the most characters out of all 5 character meals - I haven't even been to that one yet but I can see that from all the photos. And if you look at the link above, you will see the different kinds of characters you can find there.
Goofy's Kitchen has a much wider variety of food than the other character meals, but is also more expensive than Minnie & Friends. Goofy's had about 8 characters in the restaurant the last time I was there in December, but sometimes there may be 5, 6 or 7.
You will find that for every character meal, there is a camp of people who love it and a camp of people who don't. I have seen mixed reviews of Minnie & Friends' food quality and general disorganization, but other people love it there and do it every trip. I, and many other people, love Goofy's and eat there on just about every DLR trip, but there have been quite a few people who did not like it for assorted reasons.
I have a hunch that, if you are not interested in doing the Surf's Up with Mickey meal at the PPH, and if you don't need to dine with the Princesses at Ariel's Grotto, then Minnie & Friends may be the better choice for the 4-year-old and 6-year-old, but, again, it kind of depends on which characters they like, do they like to get up and dance (which they do at Goofy's), are they boys or girls, that sort of thing.
Just off the top of my head, though, I think I will say Minnie & Friends, even though my personal choice (and I think better food for adults) is Goofy's Kitchen!! Minnie & Friends has lots and lots of characters (including the Pooh gang).