Help with 3-Day Weekend Itinerary for First Visit to NYC for Couple?

Times Square is probably one of the last places a New Yorker would want to stay. However, it is central to almost all subway lines, making it easy to travel throughout the city. A few places and eats to explore based on Subway lines:

123:

Comedy Cellar - Reserve ahead of time & follow them on Twitter for hints on possible guest comedians
Big Gay Ice Cream Shop - Not your ordinary soft serve  
Wallflower  - Cute date spot for drinks

ACE:

High Line Park - Beautifully curated park to Chelsea Market
Momofuku Milk Bar - Corn Cookie, Crack Pie & Cereal Milk 
Jacqueline Kennedy Onassis Reservoir - Beautiful view of the West/East side and way to go cross town

BDFM:

Bryant Park - Place to sit down and picnic
Museum of Modern Art - Near Time Warner Center, Central Park and check out events at the museum 

NQR:

Union Square Green Market - Farmer's Market - Best on Saturdays!
Ground Zero - Commemorate 9/11 and view the museum 
Brookfield Place - Food court with endless possibilities of food and shops 

Times Square Shuttle (S) to 456:

Grand Central Terminal - Beautiful architecture and history behind the station and try the whispering arches in front of the Grand Central Oyster Bar and maybe a drink at The Campbell Apartment
Dylan's Candy Bar - Feel like a kid again with nostalgic treats 
Serendipity 3 - Famous from the movie, Serendipity and their Frozen Hot Chocolate 
The Metropolitan Museum of Art - Travel through time and be inches from historical artifacts
McSorleys Old Ale House - Oldest pub in NYC

Make sure to stop in Central Park, even if you're just wandering through.  Beautiful. Depending on your interests, you should also hit up one of NYC's amazing museums - American Museum of Natural History, The Metropolitan Museum of Art, and Museum of Modern Art are all standouts for a reason and all worth a visit, based on what you like!  Wander around the neighborhoods of SoHo and Greenwich Village to see a different side of Manhattan, and a trip down to Battery Park affords beautiful views over the water and of the Statue of Liberty.  Have fun!

3 days might seem little but I managed to pack a lot during my visit there during Christmas. We obviously walked around Times Square (it's better at night), we walked through Chinatown New York, saw One World Trade Center and 9/11 Memorial and even spent a few hours in The Metropolitan Museum of Art. Oh yes, and managed to see the sunset in Central Park.

You can find my plan here: http://aspectsofstyle.com/2015/01/09/three-days-in-new-york-city/

also now that days are longer you have more daylight to see and do things.

My favorite places for going out in NYC are Meatpacking District and SoHo. The High Line Park also starts from the Meatpacking with is convenient.

Make your way over to High Line Park and be sure to catch a sunset at the top of the Empire State Building Observation Deck!