[CCs77]

The systems with at least one station underground would be, as far as I know


-New York Area
Subway
PATH
Hudson Bergen Light Rail
-Chicago Area
El
Metra commuter
-Philadelphia area
Subway
PATCO
-San Francisco area
BART
Muni Metro
-Boston
-Los Angeles
-Washington
-Atlanta
-Baltimore
-Pittsburgh
-Cleveland
-Saint Louis
-Minneapolis
-Seattle
-Portland
-Dallas

I could have some left.

To calculate how many stations in each system are underground could be pretty difficult (good luck with New York) in other cases just one or two stations are underground.