We love the Upper West Side! We used to live there, and now we go back on the weekends. There's the Children's Museum:
http://www.cmom.org/index.html. Also, the Natural History Museum is great for kids. There's a decent cafe there as well. I personally love the Metropolitan (Art) Museum, which is a short bus ride or walk across Central Park. They have a nice library in the basement with lots of kids books, and a nice cafe, with a special kids meal that comes in a taxi-shaped box. Our favorite restaurant is Saigon Grill at the corner of Amsterdam and 90th or 91st. There's always a great vibe in there, lots of families, great food (lots of veggie/vegan options). Have a fun visit!