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Aquarium--skip. It's kind of out of the way and it's not that great TBH.

Central Park zoo-- I would just do the children's zoo, it is small and manageable! As for bikes, depends how good you are on bikes! I personally would not find that relaxing, the park can be madness on a nice weekend. I think better to do a picnic or something on the great lawn or sheep's meadow.

AMNH: fun, but very overwhelming. I would pick one or two things to see (like the whale, and the dinosaurs), and stick to that. Honestly at 2.5, LO has a limited attention span for it but prob depends on the kid.

BBP/Jane's carousel: must do! SO fun and totally age appropriate. You can also do smorgasburg--just show up when it opens.

children's museum: eh only if it's a rainy day. It will also prob be crazy on the weekend (although less so if it's nice out). I personally think the brooklyn one is better for kids under 3, but it is annoying to get to. The manhattan one is not bad, and a good option if the weather is bad.

Haven't done the MOMA or baseball game so can't speak to those! You'll have a blast!

ETA there are also a million playgrounds in central park. There's an awesome one--maybe it's hecksher playground?

ETA again that the children's museum of the arts in Tribeca is AWESOME. http://cmany.org/

The aquarium is very far away so unless you also want to do the rest of coney island(like the rides and stuff) I would skip it.

I'm not a huge CMOM fan to be honest and on the weekends is going to be crazy. Central Park Zoo is great and smaller than the Bronx Zoo so it will take you less time.

I love going to Yankees games and can't WAIT to take LO. If you can't get tickets on the Yankees website, try stub hub depending on what weekend you're going. I love doing the bleachers (cheap) but keep in mind they are very rowdy and lots of swearing.

@lawbee11: the new stadium is really nice and super easy to get to on the subway. They have a lot of crazy rules now for what you can bring in now tho so check before you go. We've had stuff taken away.

MOMA is great but pricey. The Brooklyn Museum is also great and admission is pay what you wish. It's right next to the Botanic Gardens which is beautiful this time of year. Also Bryant Park is centrally located and has a carousel and often fun things for little ones to watch/do like yoga and music. Have a great trip!

Just one thing to add:

MoMA has a kid's room called Material Lab. It's on the bottom floor and closer to the opposite side of where the main entrance is. There are activities there for little toddlers up to school-age children. If anything, it's just great to let your LO visit if he/she needs a break from the stroller. Their cafe on the 2nd floor is pretty kid-friendly too, with Trip Trapp high chairs.

Aquarium- haven't been yet but I think it's a skip...it's low on our list
Central Park-yes but not necessarily the zoo...it's really nice now for exploring/playing/picnicking
Moma- yes, my kids loved it and it's a manageable size. It's pricey but free on Friday nights (although it's a complete madhouse then)
Natural history-yes! We loved it so much! Agree with the advice to just pick a couple things to do because it's huge.
Brooklyn bridge park- the kids definitely had fun but it wouldn't be at the top of my list...I guess it depends how much time you have.
Children's museum- we've been in different cities and I feel like they all end up being pretty much the same so I vote skip.
Yankees game- haven't been but when we went to a baseball game around your part of the country actually the kids loved it!
As for FAO- my 3 year old loved it but 2 year old was pretty indifferent so depends if you think LO would be excited for it.

We went to NY in October when my son was 23 months. We stayed in Brooklyn because that where our family members live (and we were there for a wedding that was in Brooklyn). We went to the Transit Museum, Brooklyn Children's Museum, AMNH (probably only for about 2-3 hours), walked through Central Park for a bit, Epire State Building (more for my husband), and the 9/11 memorial (not museum). We were there for almost a week, but had several wedding related things to do and were pretty consistent about getting back to the hotel for him to nap every day (and he did!). Have fun! We didn't go to any zoos because we live in southern CA and have gone to four different zoos locally so it didn't seem worth it.

Not sure where you're coming from, but if you're not regularly around water in real life I'd suggest the beach at Coney Island and the Governor's Island Ferry - my LO LOVED those around 21 months. The ferry pick-up is in Brooklyn Bridge Park and there's a great splash pad nearby too.

MoMA has free admission on Fridays, I think starting at 4 if that would work for you. I'm from DC so I prefer free museum admission

Oh I missed the part about renting bikes in Central Park. I would not recommend that with a small child. I personally think biking in Central Park looks terrifying and when I used to run there I was always dodging the racing bikes going a billion miles an hour. I'm very against the horse and carriages but if that's your thing, go for it.

We took LO at 18 months. We went to Hercksher (sp?) playground at Central Park - and ran in the water features!!! So much fun. We listened and watched the park's street entertainment too. Then we did the zoo and FAO Schwarz and was a ton of fun as well. While I was working DH took LO to MOMA with a sketch pad and Liberty Science Center. That bike trailer idea sounds divine!

I will dissent about the CPZ. I took my son there recently, and it was my first trip to a zoo in a very long time. Some of the exhibits were ok but some were tiny and made me feel really sad for the animals. The penguins were especially packed in and have no access to sunlight. I really found it depressing. I am not sure how it compares to other zoos though. I may try taking him to one or two more zoos but if they are anything like the CPZ then I am going to boycott zoos.

@lawbee11: I would suggest the Roosevelt island tram--my LO looooves going on it. It's just a subway card fare, but it's an aerial tram that gives you a great view of the city and it's just 8 minutes over and you can ride it right back. Also, there's a Whole Foods not far from it, so it's a good place for a bathroom pit stop or snacks (bathrooms are in the café upstairs).