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You've pretty much named any city in the US that meets those criterion. You're set.
Although Seattle is sort of straddling the line. Not so sure about their transportation.
I just visited Seattle and almost exclusively used public trans (plus plenty of walking) and had a great time. It bumped Seattle higher on my list of "real" cities.
Seattle doesn't have a metro/subway, but does have a nice bus system, and their downtown transit tunnel lets the buses skip traffic in the densest part of town. Plus, starting in a few weeks, they'll have light rail transit through that tunnel. They also have ferries, which are a blast in- and of-themselves, and all the downtown buses are free within a "free ride" zone (during certain hours, anyway).
I've visited cities as PART of my vacation, I can't imagine spending an entire vacation in a city.
But then I'm not a fan of cities.
It depends on the city. I enjoy cities and can easily vacation in NYC for days.
However, there are certain cities and regions of the country, that if you don't get out of the 'city' then you are shortchanging yourself.
Seattle and the cities in Northern California are good examples of areas where the landscape and outdoor environment is just as part of the cultural experience as the cities themselves. I'm much richer for the experience of renting a car and driving down Highway 1 in Northern California had I been if I had just stayed in the city.
Washington DC is also a very good "city" vacation. We visited there a few years ago. Just checked into our hotel in Arlington, caught the Metro into the city every morning and rode it back every night. A great week vacation.
Based on your criteria, I wouldn't touch Miami, Atlanta, Houston, Dallas, New Orleans, or Los Angeles and it's mostly because they don't fit all three of your criteria.
I strongly disagree about New Orleans. It's a relatively compact city and you don't need [want] a car in the French Quarter. There's plenty of foot traffic at all hours in the FQ, which perhaps is the most pedestrian-oriented neighborhood in the United States. Want to explore more of the city? The Charles Streetcar is a fast and convenient way to take you from the Quarter/Downtown to the Garden District/Uptown. They are absolutely gorgeous neighborhoods and are great for walking. Magazine Street is a very pleasant shopping street to stroll, but for some reason, seems to be often overlooked by visitors. Going in a different direction, the Canal Street streetcar will take you to the northern edge of New Orleans, where you'll find City Park. After that, take the ferry across the river to Algiers Point or step a few blocks just outside the Quarter to Faubourg Marigny where you can take in great live music on Frenchman Street.
NOLA may not be as cosmopolitan as San Francisco or Chicago, but it's definitely worth a visit for someone looking for a city vacation. What it lacks in sophistication, it makes up for with a culture, history, atmosphere, and general aural that is uniquely New Orleans. You won't mistake yourself for being anywhere else when you're in that city. Everyone I know who has visited New Orleans (myself included) has not rented a car, walked everywhere, and thoroughly enjoyed what is truly one of the "treasure cities" of the United States.
I'd add the following North American cities based on my experience:
Miami Beach (South Beach in particular)
Toronto
Quebec City (no need for a car if you stay in the city itself)
Was DC mentioned? I don't recall.
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