I'm an ortho wife who has lived in New York the past 8 years, the first 5 in Manhattan, the last 3 years in an outer borough.
My friends, church and work are ALL in Manhattan, but my hours are pretty reasonable, and if I go out late with the girls, I always have a place to crash for the night. It's no big deal for people with typical day jobs to commute. Residency is not a typical day job, and while investment bankers and corporate attorneys sometimes work around the clock and live in the 'burbs, I'm pretty sure residents don't get towncars from their employers to take them home when they work late.
If you match in New York, you will want to live very close to the hospital at which you will spend the most time. Most if not all ortho residency programs in NYC have resident housing at reasonable rates for those neighborhoods. I also found that the pay, on average, is notably higher than programs in other parts of the country, even when you account for taxes.
What specifically are your wife's concerns about living in Manhattan?
If she wants a big apartment/house, then you can cross the Manhattan programs off your list (but keep LIJ on it).
If she wants a yard, there are tons of parks and apartment complexes (such as Stuy Town / Peter Cooper Village, really close to HJD) that have courtyards that you can enjoy without having to maintain.
If she's thinking kids in New York might be difficult, that could be a valid concern, but I guess you'd have to tackle what particularly concerns her about having kids in New York. Is it logistics? Money? Safety? School quality?
If the concern is money, it's probably not as bad as you're anticipating. First, you would get rid of your car(s). No more car payments, no more insurance, no more gas. An unlimited monthly metro card is $89/month. And if you live within walking distance of your hospital, you will barely spend any money on the subway. There are also tons of *cheap eats* places that offer some of the best food in the city (Mamoun's, I'm looking at you!). There are often free or inexpensive concerts and theatre events. Services that are luxuries elsewhere (tailors, cobblers, manicurists, etc.) are so common here that they're often very reasonably priced. Plus, if she works, her salary will likely be much higher in New York than it would be elsewhere.
If the concern is saftey, stick to NYU, Mt. Sinai, Lennox Hill, St. Luke's-Roosevelt, and HSS in Manhattan. I love the area around Columbia/NY Presbyterian West; Washinton Heights is awesome and so full of character and life. But, it is a little more removed and closer to Harlem. The neighborhood is still better than most cities in the US, but I could see how someone concerned about safety might be hesitant to move there. The others are all in gorgeous $$ locations (Columbus Circle, Upper East Side, Grammercy). Obviously you need to be aware of yourself and not make bad choices (like walk around alone wasted at 2am on a Tuesday morning), but the stats have shown time and again that New York is really safe.
Good luck with the whole process! I love New York, and I think there are a lot of misconceptions out there about the city. Still, it's not for everyone, so if it's not for you guys, don't waste your time and money applying here.