My experience in Boston was pretty nice, the lounge is very comfortable and a great space. Although I the main hall area wasn't extremely impressive.I would say my favorite big-city station is actually Boston. It has a great lounge, nearly everything in the station is on one level, it's easy to navigate and offers high-level boarding on every track (my biggest qualm with Washington DC and Chicago).
And I've been in parts of it the public doesn't usually get access to, like the tunnels underneath and the attic.
Portland is my home town favorite going back to my great-grandparents' travels. I've spent hours there, whether waiting for a train or on work or just observing.My favorite is Portland, since it's the one that lets me ride. And it's a lovely station that's changed little as the city has changed around it.