My boys attend Church of the Incarnation (COTI) on McKinney (near West Village) twice a week, and have been going there for 2 years and love it! The MDO program has longer hours and cost less than most MDOs. They attend 9am-3pm (many are 10-2), T/Th, and we pay $385/mo for both. Summer registration has begun and it fills pretty quickly.
Let me know if you have anymore questions.