The Insight guide to NYC is good for breaking things down by neighborhood. The restaurants around Times Square tend to be chains and geared to tourists and are generally not that great. Restaurants are expensive in NYC and it's worth doing some research ahead of time. I know that a lot of posters complain about the high food costs in NYC (not to mention the whole tipping thing), but researching this ahead of time will definitely help. Someone up above mentioned Grand Central--they have a great food court there.
You didn't say how late in October that you were going to be there, but if you are there on the 31st, Bryant Park (small park outside of NY Public Library) has holiday kiosks for shopping. If you are into shopping or have a special interest, check to see what's available In Manhattan, there are 3 separate bookstores that carry only cookbooks, for example.
The kids may like the NBC Studio tour in Rockefeller Center. They can see the tv sets and how things are filmed there. The small, but historic ice rink opens at Rockefeller Center on Oct. 7.
Also, if you are there over Halloween, Greenwich Village has what is supposed to be a really good Halloween parade.
Roosevelt Island can be visited by a tramway, which your kids may enjoy. There isn't much there that would be of interest to kids, but there are good views of Manhattan.
Love the High Line. Unfortunately, so does everyone else. Off hours it is less claustrophobic.
There is a new amusement park out on Coney Island that the kids may enjoy (Luna Park). I haven't been there but the reviews of the park seem to be good. The staff, however, are famed for rudeness, so take that into account.
Times Square should be avoided during the day and in the evening prior to the Broadway shows starting up. But it is nice to sit in the bleachers there after 8:00 and see all of the gaudy neon.