Trip to NYC...suggestions?

Not a resident, but have visited many times....
Hmmm, some basics:
Times Square shopping...take it all in
Children's Museum
Carriage ride through Central Park
See a show on Broadway
See the 9/11 Memorial
Statue of Liberty

To experience the city:
eat in a diner
visit the neighborhoods (Greenwich, Upper East Side, Soho, Meatpacking)
grab a dog from a street vendor
buy "street bling" (aka: fake bags, sunglasses, Rolex) and haggle!

Bring the strollers, pack lots of snacks. Leave the carseats, if you can, and take the train.

Don't take the Circle Line, it's a rip-off. Take the Staten Island Ferry! It's free!

There's a Toys R Us near Times Square that has this really cool INDOOR ferris wheel, each car has a dif theme e.g. Toy Story. Other than that, I would avoid Times Square unless you're seeing a show, way too crowded with tourists.

If Queens is convenient for you, I highly recommend the NY Hall of Science, which is really a children's museum. It has an unusual outdoor playground, a toddler area which would be great for your kids, just a ton of stuff, and is much less crowded than other NY attractions

If it were me, I would try to incorporate a park, playground, or other kid thing into every day so that your 3 year old won't go out of her/his mind doing all the adult stuff, e.g. there's a cute park in the West Village

I wouldn't take a stroller, such a pain to get around with it, and you will be in and out of taxis, buses and subways so there will be ample time to sit. Hopefully you are still able to carry the 6 month old in a sling or something similar (?)
Staten Island Ferry, it's free! And it's a great way to see the whole harbor.
The Natural History Museum and Central Park Zoo are great. If your 3.5 year old is a girl, visit American Girl Place, SO fun!
Walk around Times Square at night and be sure to have at least one meal in Little Italy, yum. And make a point of visiting Grand Central Station, it's an American icon, beautiful!
I hope you get a chance to go out with your girlfriend and see a Broadway show and maybe go shopping (even if it's just window shopping.) You are going to have a BLAST, I'm jealous, I LOVE NY, have fun!!!

Pack a lot of patience.
Don't leave the apt till after 9:30, don't plan on returning any later than 4pm. Kids in rush hour are just plain rough.
Think hard about sorting out bathroom stops as publicly accessible toilets are few and far between (starbucks is usually a good bet).
May is a great time of year, enjoy your stay.

I would definitely bring either 2 strollers or a double stroller. I don't care how much your 3 year old likes to walk, NYC is a different animal. The streets are crowded and walking out into traffic is very hazzardous.

What kind of apartment does your friend have? Most NYC apts are very small. Where will the kids be sleeping? You'll definitley need a Pack and Play for the baby, or something similar.

The Circle Line is lots of fun and your 3 YO will like being on a boat. Also do the 911 memorial and then go to Chinatown for lunch or dinner. There will be lots to look at for your little one. Also, you can eat on Mullbury St. if you want to experience Little Italy. Or just get dessert - yum.

Take a walk over the Brooklyn Bridge and have pizza in Brooklyn. Cab or Subway it back. If you've bnever been on a NYC Subway, you must go for a ride.

Take a day to catch a show (perhaps if your friend is super cool she will watch the kids while you are enjoying an adult Broadway show with your hubby). Go to Top of the Rock or Empire State Building. Try the Museum of Natural History, too.

There is so much to do that you will have to narrow it down. Plan ahead if you want any tickets. I think it's better to spend a little more rather than wait on a two hour line for cheaper tickets.

And May is beautiful in NYC - definitley go to Central Park and go to the Zoo. Or, go to the Bronz Zoo - it's awesome. And just a subway or bus ride away. Go to a Mets game (cheaper and easier to get tix than the Yankees).

And by all means, get a hot dog (dirty water dog) and pretzel from a street vendor. Delish! Street food (aka Street Meat) is all the rage now (6th in the 50s) don't be afraid to try it.

Have fun - there is so much to see. And buy a Time Out NY when you get in.

Haha - I agree about the bathrooms!! All hotels have great bathrooms - but I heard that Starbucks is closing bathrooms to the public.

I've never taken the kids to NY but we fly with them. Borrow as much stuff as you can from your friend there, pack'n'play stroller etc so you're not flying with so much stuff. I'm so jealous! Can I join and help out?? ;)