While their website does not specifically mention special needs kids, the following recommendation is from a parent:
Chess class starts next week! Bay Area Chess has a great class for kids 5+ (special needs kids welcome!). Tuesdays from 10-11 at their offices in North San Jose. Students must have some basic knowledge of chess (how the pieces move) but do not need to be good players. $135 for 6 weeks.
My son is homeschooled and has HFA/ADHD/Learning disability in math and has taken classes with them for 3 years now and I HIGHLY recommend!!!! The teacher, James, is great with kids and very patient and fair.