This is OP with an update. We are staying here:
http://www.vrbo.com/231909
Only two bedrooms, but we can stay for three nights and my daughters (I'm now bringing the 7-year-old too) will share the sofabed in the living room.

Itinerary is still in progress but it looks like we'll do Empire State, AG store, either Matilda or Rockettes, and at least one museum. Kids are lobbying for Statue of Liberty too but I think we'll need to see how the weather is.

Thanks for all the great ideas! I am still working on an itinerary but will post here once I figure things out. It's now looking like I might also bring my 7-year-old girl, which probably won't change things too much. My dad is in charge of the VRBO reservation but if we find a good one I am happy to share it here.

Matilda the Musical. I saw it in London in a theatre packed with 10yo girls. And now it's in NYC!

Out of curiosity, have you been successful in finding a 3 BR VRBO that will do only 3 nights? I see more like weeklong minimums. It seems like a good idea but wonder if this is a feasible option.

The Tenement Museum was amazing. I took my 8yo DD and we both loved it. Lion King is great but it's coming to DC this summer so maybe something that won't be in DC any time soon. Wicked is wonderful. Or you can take your chances at TKTS and see what you can get for a decent price. My friend who lives in NYC with her 9yo has suggested Alice's Tea Cup for us, Dylan's Candy Bar, etc. My kids love to wander through some of the specialty stores like Lego (smaller than you think it is so a quick stop unless you're completely Lego crazy), M&Ms, etc. All right around each other and near AG. Maybe she would like skating at Rockefeller Center?

Hey OP, when you get your itinerary, can you please post it here? We are going in the spring also and I am wondering how to fit it all together.

And any PPs who have a suggested itinerary; I bet OP would be as interested as I am in reading it.

Penguins at Central Park zoo.
Tenement museum on Orchid st.
Brooklyn museum

ride the subway
Today show at Rockefeller Center
Newsies or Lion King on Broadway
Levain Bakery on the Upper West Side not to far from the Natural History Museum for THE BEST chocolate chip cookies!

there is a recent thread that has basically the same question - maybe it was a 13 yr old girl - but lots of good ideas on it!

M&M store and Lego store were huge hits with my girls!
For a show - we loved Cinderella
We did Top of the Rock instead of Empire
Photos on the steps in Times Sq.
Shake Shack burgers
Statue of Liberty
Central Park remote sailboats

Serendipity for ice cream (if the polar vortex has left by then)

Ellen's Stardust Diner.

Alice's Tea Cup

My 10-year-old daughter and I are meeting my dad and grandma in NYC for a three day weekend in late March. I haven't been to Manhattan since before DD was born. Trying to decide what to put on our agenda (and accordingly where to stay; we will look for a 3Br VRBO that fits all five of us). Besides the American Girl store, Empire State Building, a play, and either the natural history museum or the Metropolitan museum, what do you think a girl this age would love to do in NY? Thanks for your suggestions!