Will we have enough time to go into Amsterdam

Yes you will 3 hours more or less since you would have to go through passport control coming in and going out and through security coming back in. Assuming your flights are all on one ticket, why would your bags not be checked all the way to JFK?

I would start making my way back to the airport around noon for a 15:25 departure

Are you on a single ticket?

I ask, because I could not find an itinerary that matches your description. If separate tickets, you will need to retrieve your luggage and check it on to JFK.

What does your AMS-JFK airline recommend for arrival time before the flight?

We arrived in Amsterdam at 6 am and departed at Noon. We had ample time to hop on the train and walk through the streets and see the canals, have a coffee at a shop, stroll next to canals, and we rode a canal tour that departed near the train station. We got back in great time. They have large storage lockers in airport where we stashed our carryons.

You will not have to go through passport control (immigration) arriving from Prague, as both the Czech Republic and the Netherlands are in the Schengen Area. When you arrive you can just walk off the plane. I estimate you could be at Schiphol station by 9.

Departing you will have to go through security and Schengen Area exit passport control, plus abide by any minimum times set by the airline. I would want to be back going through security 13:25 latest. But double-check the airline website.
And, if this is two tickets you will need to pick up your bags, and check in again, which needs more time.

So, in theory, you could be at Amsterdam Centraal station 09:30 to 10:00, and leave again 12:30. Enough for a quick glimpse.