We didn't book at Ellen's just walked in. While we were there a queue developed and disappeared again. I'm not sure you can book but I would be prepared to queue for a few minutes for the experience and be prepared to put a note into the bucket for their music lessons/acting lessons fund.
As others mentioned - we went into and up the Guggenheim but there was very little of interest in the current exhibition and virtually nothing of the permanent collection. We've visited Peggy Guggenheim in Venice and Bilbao and this (bar the exceptional building) was a very poor third.
We tried to do MOMA the first time we visited but the ticket queue was almost a block long. Note the ticket queue, if you were prepaid you could walk straight in.
We went last time with the City Pass but we weren't massively impressed - a whole floor was out of action for renovation. Their definition of Modern Art seemed to stop at 1969 which was a bit disappointing.
The Museum of Art and Design (MAD) was also a bit odd and slightly underwhelming.
The Whitney Museum at the end of the Highline was a much more interesting visit.
Again this all depends on how much you're into Modern Art

As we also visited DC where all the museums are free and massive that may have coloured my memory of NYC where they all wanted an arm and a leg admission.
The taxi ride from Penn Station to the Roger Smith Hotel was 1.5 miles. The taxi was a Ford Crown Victoria, what I think of as a "real" NYC yellow cab.
I had to load and unload our own luggage, he made us sit 3 across the back seat. Despite being gigantic there was a plexiglass screen between the seats so I had less leg room than I do in our Mini (I'm 6'2").
We crawled through the traffic and it took about 1/2 an hour. I don't remember how much it cost but I do remember it made my eyes water - coupled with the guy not wanting to give me a receipt (which I wanted as a souvenir) and refusing to put the amount I paid on it, just the metered fare.
I suspect he thought I was going to complain, I wouldn't have minded the traffic or even the fare if he'd been less of a git about the whole thing. Arriving in NYC should have been exciting but he just made me cross and feel ripped off.
We walked back from the hotel to the station towing the wheelie case and it took less time
If you haven't see it you might want to look at The Ride. We didn't do it but saw the bus on its rounds and it looked like fun - more than the open top tours. When we were there it was scorching hot, so the air con appealed. When you're going the heating might also appeal
https://experiencetheride.com/