I'll be in NYC for 2 days and Boston for 2 days.
Recommendations on attractions to check out? I am not super into the touristy stuff, but wouldn't mind checking out some local hotspots and restaurants/bars.
The WTC museum
Statue of Liberty
If you like trains, there's the Train Museum.
Walk across the Brooklyn Bridge?
You can keep yourself busy for 2 days Just in Manhattan and Brooklyn, so unless 400,000 Italian stereotypes are your thing, don't bother coming to Staten Island.
That being said, if you like to eat, and don't wanna go broke doing it, hop on the ferry for free and come on down.
Goodfellas is a local landmark, and is superb.
.....just dont eat your pizza with a fork, this is NY.
Save that for Chicago, the pizza you can kill someone upside there head with.
New York is all about the shoe leather! Just walking up- and downtown Manhattan for a day is awesome. If you look up at the skyscrapers you'll be marked for a tourist but there are so many others it won't cause you trouble.
If you eat at McDonalds there are big signs everywhere saying you only get 20 minutes, and watch your valuables. You'll have to share your table with a stranger too.
Read up on http://forgotten-ny.com/ as there's stuff there I'd go see now for grins. They turned an abandoned highline rail system into legit nature paths, taking away some coolness, for example.
Central Park, the Highline, Landmarc restaurant overlooking Columbus Circle. Rent a bike at the shop on 72nd Street near West End Avenue and ride the Riverside Park bike trail south to the World Trade Center area. Take in the World Trade Center Memorial if you have time. There's a dingy little bakery on 74th Street near Amsterdam, Levain Bakery. Many think they bake the best chocolate chip cookies in NYC; four bucks each.
* Freedom Trail. Ties together many sites from the War for Independance. Boston Common, Paul Revere's home, the USS Constitution, site of the Boston Massacre, Fenuille Hall.....
* Great Italian restaurants in the North End where you will be following part of the Freedom Trail. More than I can name along Salem St. Ask the locals when you are in the area.
* West of the Boston Common is the Back Bay area. Shops and pubs.
* Arnold Arboretum in Jamaica Plain is great for an afternoon of hiking.
For Boston, you can also check this thread that I started a few weeks ago before our trip to Boston, and the recommendations I got were very good, and we managed to cover most of it I think:
NYC is a big place, so I'd split it up. Probably the first day go to wtc, TriBeCa, Chinatown and anything else downtown (battery park, perhaps the circle line over to the Statue of Liberty). Depending upon what you decide, then on day 2 do say from say 30th st uptown. Going up to 58th or 60th is managable.
I like 30 Rock versus Empire State Building.
Grand central station is pretty magnificent. Same for the public library, and the met/natural history museum/cloisters.
Street food, certain buildings and stores, good restaurant, and a good view are all considerations.
In boston, I'd try to get on old Ironsides and go through the old market downtown. Walk along the Charles to get the view. Check our Paul Revere's house.
Museum of Natural history has cool stuff. The staten ferry or there is a boat tour all the way around Manhattan island that is interesting.
THe naval museum ships, I don't know what they have there now but they had a aircraft carrier you could tour, as well as a few sailing ships. Some of those kinds of attractions sometimes move around so you'll have to look that up but of course being major ports both cities will have marine exhibits.