Steve, Joe's, Keste and John's are appealing because of their proximity (Scott does a walking tour), but, as far as must-taste pizzas go... I hate to sound like a broken record, but they leave a lot to be desired.
Keste is definitely worth a trip, but... it's the same owner as Don Antonio (Roberto), so the pizzas will be pretty much identical. Don Antonio is actually larger, so they have a greater selection of specialty pizzas, including the Montanara (fried pizza). Don Antonio is right in the theater district, so, if that's where you're staying, that's the easiest to make happen. Don Antonio also has pretty late hours and is open from lunch to dinner. Based upon where you're staying, D.A. is a no brainer, imo.
Once you remove the need for a trip to Keste, you're left with Joe's and John's. Scott's bus tour is open ended on the locations it visits, but I can guarantee you that it will hit at least one of New York City's legendary coal places. As far as NYC coal goes, John's is towards the top, but coal, for the most part, has been coasting on it's laurels for decades. Juliana's is showing some promise on the coal front, but logistically, I'm not sure how you can make Juliana's happen. Still, though, you absolutely don't need to visit two coal places when you're here. Go where ever Scott takes you (most likely Lombardi's), soak in all of Scott's historical brilliance and deal with whatever quality of pie you're served.
And then there was Joes. Please please please don't make the trip to the village just for Joes
If you're down in Battery Park for the Statue of Liberty tour, a subway up to the village is not that different from a subway out to Williamsburg (about 10 more minutes to Brooklyn). Williamsburg Pizza is just around the corner from Forcella and both are about a mile from Motorino. A mile might be a little too long to walk with the current weather, so I might do a taxi for that- or just do Forcella and Williamsburg.
At the end of the day, Don Antonio + Forcella + Williamsburg + Scott's tour will be about a thousand times better than Keste + Joe's + John's + Scott's tour. This part of Brooklyn isn't too terribly scenic, but you've got the rest of your trip for that.
A subway to Brooklyn gives you the best pizza that NY has to offer, while still working within your limited schedule.