I'm sorry you missed seeing Peter Pan. He is frequently seen in the parks. I have seen him in a variety of places over the
years, including on Main Street in the Magic
Kingdom and near the Peter Pan's Flight ride. His current guest
greeting area is just outside the Pirates of the Caribbean ride, where
you will also often see Hook and Smee too. When you enter the park,
pick up a free Times Guide, which will be located near the maps. This
should tell you when Peter Pan will be greeting guests at this
location. If for some reason this is not listed, just stop by the guest
relations office at any of the theme parks. Ask them to call the
"character hotline" for you and they will be able to tell you where and
when any specific character will be in the parks during your stay.
While they are not on the official schedule, I have seen male
characters at breakfast at Cinderella's Royal Table a few times
including Peter Pan, Aladdin, and Prince Charming. If you were already
planning to dine at CRT, this might be a nice surprise to happen upon, but I would not schedule a CRT visit specifically to see Peter Pan, as you'd likely be disappointed.
My most notable interaction with Peter Pan occurred during the
Family Magic Tour (we've taken it twice, we had such a great time). You can read more about my experience with Peter Pan on the tour
here.
I also had a nice experience with Peter Pan at the end of the Pirate
and Pals Fireworks Cruise I recently took with Moms Panelist Cathy and
her family. You can read Cathy's description of the cruise
HERE.
Hope you have a magical vacation!