You are welcome to take pictures of Jake during the show, but unfortunately I haven't seen him in the parks just yet. You will be able to see Mike and Sully, though! They are in Hollywood Studios, along with other Pixar and Disney characters (see complete listing
here).
Captain Hook, Peter Pan, and Mr, Smee are a little harder to track down. I have seen them in both Hollywood Studios and Magic Kingdom in the past, but neither very reliably. If you really want to see them, I suggest booking a
Pirates & Pals Fireworks Voyage. Not only will you get a guaranteed greeting, but you'll have far more opportunity for personal interaction as well. I have wonderful pictures of Captain Hook holding my daughters' hand and escorting her from the resort out to the dock, and even helping her board our boat! It rained on our cruise the night we went - a monsoon-ish, very heavy rain! - and we still recall it as one of our favorite Disney memories. I highly recommend this special experience, and if you have a little pirate fan, I think she would treasure it as well.
Hope that helps!