I don't know your budget, but if you're traveling with an 11 year old son, I'd stay in mid-town, near Times Square. Kids like that area as it has fun and diverting things going on (the lights, toy store, Midtown Comics), it's got kid accessible fast and sorta fast food, and it is convenient to pretty much everywhere else you're going to go either by taxi or subway (for kid recommend the Central Park area attractions of the Met - especially Egyptian temple, Museum of Natural History, Zoo, etc.). Adults like that area because it is near the theaters, has good restaurants and bars within walking distance, and you can find nice hotels. Personally, I often stay at the Sofitel, but there are places for every budget including a giant Marriot.
If you want someplace more hip, try the meat packing district. It's got the high line, the Whitney Museum of American Art, lots of good bars and restaurants, and is near some of the touristy stuff on the Hudson warterfront (Chelsea Piers, etc.). I tend to stay at the Gansevoort Hotel in that area, but the Standard Hotel High Line is supposed to be good.