The Conrad is my current favorite: all rooms are two-room suites, classy, excellent service, and Shake Shack is right downstairs at the corner.
The Conrad is in lower Manhattan in Battery Park City, close by is the new Brookfield Place shopping/dining area. We've seen celebrities staying there and the paparazzi out front. We know the subway system so to us this is a great location.
We've stayed many times at The Millenium and received every time a suite upgrade as HH Gold. Lower Manhattan, but good location, and easy to get to the WTC Memorial and the new Westfield shopping mall.
Haven't stayed at the NY Hilton Midtown in recent years but always enjoyed its tourist attractions location. We never received room upgrades there, though.