In the parks, Guest Relations has Braille guides you can borrow. My sister got a kick out of these, and how detailed they were. In addition to the normal guidebook kinds of things, they also gave details on how to move from one place to another, and interesting things to "see" with your hands.
I'm not sure if places other than the parks (Fort Wilderness, the hotels, Downtown Disney, etc.) would have similar guides. If so, these might be a fun way to spend some time. Because the guides are so detailed, it might be a thrill for her to be your tour guide.
When my sister and her family join us at WDW, she's just another member of the group despite being totally blind. She enjoys everything we do. Eyore's her favorite character, so we always need to do Pooh's ride. We also need to go through the Pooh store thoroughly each trip to inspect all the stuffed animals and merchandise, and of course, have a meal at the Crystal Palace. Even rides that are especially visual, like the 4-D movies and the like, are still enjoyable for her. She gets into the story, the music, and hearing the reactions of the audience. Whichever of us is closest will also give her some descriptions of what we're seeing.
If your niece is into shopping, spend some time at DTD with her. If she's into princesses (probably wouldn't admit it at 16), explore the new princess room at World of Disney. How about a beauty day at Bippity Boppity Boutique?
As guests at Fort Wilderness, the Disney Transportation network is open to you. Most of the time, we only think of boats and monorails as a means of getting to a park. But, it can be fun to just take a ride. (Also, since you'll have time, you can ask to wait for an opportunity to ride with the pilot.)
There are some clubs at Pleasure Island that might be fun for a teenager. Does she have similar aged siblings or cousins? Maybe they'd even enjoy a night of adventure away from the adults. The Boardwalk is another place to explore and have fun.
