I've been to both John's, Bleeker and Times Square (the Times Square location is a great place to hit with a bunch of kids in tow that won't break a budget unlike most places in Times Square) and the original Pepe's is better. That said, I have Modern over Pepe's original in my book followed by Bar then Sally's.
Back in NY, I actually hold Sottocasa in Brooklyn right off of Atlantic in high regards, especially for their old school sausage pie. If you're going to an event at Barclay's instead of MSG, there's a Patsy's on Flatbush that is also good to for kids.