My wife and I visited New York this past summer...we stayed for about 4 days, so we had a little more time to work with than you did. Here was our takeaways.

1. While the trip had its good, we will not return. Of all of our vacation locations, this was our least favorite. We spend 4 days in Boston, followed by 4 days in New York. Boston was a thousand times better. We were amazed at how trashy NYC was with the homeless everywhere, trash bags stacked up 10ft high, and just litter everywhere in general. Boston was a much cleaner place...more high class feeling. NYC is just bombarded with tourists who don't give a shite and we felt like that's what led to us not liking it quite as much.

2. We took the subway or walked everywhere we went. We never once got in a taxi or on a bus at either city. We thought it was incredibly easy to figure out, especially using Google Maps or the Map App on iphone. They both do a good job of telling you where to board, which train, when to swap trains, etc. The New York subways were newer looking and cleaner than Boston's. We also booked a hotel that was near Penn Station, since it has access to all parts of the city via subway. We were within 150 yards of Penn Station so walking to/from the subway was easy...just really convenient in general.

3. For food, skip the street vendors. They suck and are overpriced. You're gonna pay no matter what you eat in NYC (unless you're just searching out cheap/fastfood areas)...might as well get quality. We found local diners and such for most meals. Don't be afraid to ask locals for suggestions...they will send you to smaller locally owned places which aren't so commercialized and are usually pretty dang good. I specifically remember John's of Bleecker St (pizza joint) which was awesome. We ate at Keen's Steakhouse one night which was very nice. When in Chinatown, the best place we ate was Shanghai 21. I've never had real Chinese like that...it was great.

4. We spent one day exploring the scenic areas and shopping. We walked about 12 miles this day, all the way from our hotel up to Times Square, then walked over to Fifth Avenue and did lots of shopping there. Finally took the subway back to the hotel. We left the hotel that morning and made it back around 6 or 7pm, then went to eat.

5. We spent one day in the Bronx. We went to the Bronx Zoo, then went and saw Yankee Stadium. They were having an away series, so we couldn't catch a game. We did go into a few of the local bars near the stadium and ate/watched a game on TV with some of the regulars, who were very cool and gave us some other areas to check out.

6. We spend one day in the southeastern section of Manhattan. We saw the 9/11 Memorial, went to the Trade Center Mall, rode out on a ferry to the Statue of Liberty and Ellis Island, then walked around Battery Park, Tribeca, Soho. Just checking out local stuff and seeing what we can see. We aren't huge fans of the big bright lights and commercialized areas you think of when you think New York. We preferred just seeing how the regular folks around there live.

7. We spent one day exploring ChinaTown in the morning/lunch time (my personal favorite part of the whole NYC trip) and walking the Brooklyn Bridge. Chinatown was very clean. The people were friendly (though you will have to tell 100x people you don't want to buy their fake Louis Vuittons and such). The food was good, even the little snacks and noodles we got from street vendors. After walking the bridge, we took the subway from Brooklyn to Coney Island (long arse ride), got some Nathan's hotdogs, walked the beach some...once again, we were turned off by the quality of people there.

So long story short, we just weren't that amazed by all of the lights and attractions most people think of...we were turned off by the trashiness and some of the people we encountered. Lots of good found if you look in the right places. Way too much to see and do. you've got almost no chance of getting it all in 2 days.