You guys are NUTS! Longshot, I love you bro, but Forbidden Planet is by far the best comic book place in NYC! Granted I am sure the London one is better, but the Union Square place rules. I've gotten so much shit from them and the staff is so cool. Atmosphere is way better than Midtown Comics too. And Nailz, idk whatcha talkin' about duder, but the Guggenheim is the best museum in the city. Every time I've been there I've seen amazing stuff.
Food-wise, as Longshot said Katz's rules, but it's kind of touristy. Definitely try Shake Shack if you're into burgers. Arguably the best burger you will ever have, end of story. They are scattered all over the city now so finding one shouldn't be too difficult. Warning though: be prepared to wait on a long line if you're going to the one in Madison Sq Park or the one in Midtown. The one on the upper east side is your best bet regarding the lines. I recommend the shack-stack for first timers. If you're into Japanese food, Momofuku Noodle Bar (technically, Momofuku is Korean and American influenced as well) and Ippudo Ramen are the best places IMO for Ramen, which is amazing in the cold Winter months. Of the two, I prefer Momofuku because they have better pork buns (you MUST try these if you go there, they're small and you get two of them so you can split them if you want) and they make their own soft-serve ice cream which rules as well. For Sushi and other Japanese foods on the more authentic side of things St. Marks (which is now called Japan Town) rules as well. For Pizza, you can pretty much go anywhere for a decent slice, but the REAL stuff is in Brooklyn. Di Fara's in the Midwood area is one of the oldest running "classic old school" NYC pizza places that hasn't sold out to corporate chains and the same guy comes in every day and spends 12 hours making pizzas for hungry patrons, and has been doing so for about 40+ years if I'm not mistaken. Lucalli's Pizza in Carol Gardens is a relatively new place, but is arguably the best pizza place in the city as well. Also fyi, all of these places are relatively in-expensive. For mid to uppier tier restaurants: David Burke's Townhouse, Aquavit, Shun Lee (Linc Center one only), and Peter Luger's are all worth it if you want to spend a little extra.
Idle Hands and Duffs are two metal bars that are cool spots if you're into that sort of thing. There are also alot of cool bars on North 6 st in Williamsburg, Brooklyn. Central park is always really cool to visit anytime no matter what. Times Square is cool at night, but it's not really cool for more than 10-15 minutes and is otherwise annoying and crowded. Gotham Comedy Club and Carolines are two cool comedy clubs if you're into that. If you wanna catch a movie, my two favorite theaters for mainstream films the E-Walk in Times Square and the Lincoln Center AMC. For indie films, the IFC theater on the lower west side is AMAZING, and so is the Film Forum on Houston. You should also probably visit Rockefeller Center and go way downtown to the ground zero/memorial area. Union Square has a lot of cool stuff to check out as well. The Museum Of Natural History is cool. Coney Island is cool too, but not so much in the winter. If this was the Summer, I'd probably highly recommend you go there, as well as the Brooklyn aquarium. The Bronx Zoo is awesome any time of the year.
Some people recommended going to Canal St. I honestly have been there a bunch and it's kind of boring. If you want a cool fake watch I guess it's fun, but there are better things to do with your time if you ask me.
So yeh, that's all I can rattle off at the top of my head. Take it from me though, a real New Yorker ovah heah.
edit:
Taxis are pretty in-expensive by and large and you can get them fairly easily anytime except for 4-6pm and even 9-10 am. During these rush hours, it's pretty difficult to get a cab, so you should have some familiarity with the subway. The subway looks way more dangerous than it is, and I guarantee you will see a homeless dude on the train giving you his story and asking for money. Don't get freaked out by this, they are harmless. The only time I would say to be careful on the subway is after 12 am in the other boroughs. But again, you could easily catch a cab at that time if you wanted to anyways.
Maybe you should just come to NYC instead 
