You will want to contact an Accredited Member of the Stained Glass Association of America. Any of these studios are qualified to assess your windows and give an estimate for repairs and restoration.
You can find a list of Accredited studios online at:
http://www.sgaaonline.com/articles/selecting_a_studio.htm.
You can also find the Stained Glass Association of America's
Sourcebook online at
http://www.sgaaonline.com/pdf/Sourcebook.pdf. This publication is designed to help people with finding a studio for either new work or restoration, and the book has articles that you may find useful.
If you have any further questions, feel free to contact the SGAA Headquarters directly at 800.438-9581.