At Sleepy Hollow, I am pretty sure you don't get a choice. It is just two chocolate chip cookie and a hunk of vanilla ice cream...wonderful though. I believe at Main Street Bakery you get a choice or you used to of cookies and ice cream, but I am not sure what the choices are excatly.
I am not aware of this being offered at any other parks other than MK. You can get premade ones at ice carts and stuff. They used to serve the homemade ice cream sandwiches at Chip and Dale's cookie cabin, but I'm not sure that is open anymore. Last time I was there it appeared closed.