I've pulled together every mention of every tunnel (except the BR&P one which is an active road underneath an abandoned railroad -- but there are a LOT of tunnels underneath abandoned railroads):
O&W
Northfield
Fallsburg
High View
Hawk Mountain (west end destroyed, east end buried)
LVRR
Short tunnel under the NYS Thruway on Rochester Branch (arguably a bridge)
Tunnel under one of the Buffalo airport runways on the Niagara Falls Branch (converted to automotive traffic?)
DL&W
Tunnel to coal dock at Oswego
Willis Avenue to West Shore bridges under NYC (very long run of plate girder bridges now dismantled)
RW&O (NYC)
Tunnel in downtown Oswego
Rochester Subway
Tunnel Court Street to Brown Street
U&D
Kingston under Delaware Ave
NYC
under NYS 92 west of Cazenovia ( 42.945 -75.887 )
St. Mary's Park in the Bronx
New Hamburg
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Boston and Albany
Under Tunnel Hill Road (42.390 -73.467)
Little Falls under NY-5 for the Dolgeville branch
Troy Union Railroad (in turn owned by NY Central, D&H and B&M)
5th Ave behind The Market (destroyed)
LIRR
Atlantic Avenue Tunnel
Park Avenue Tunnel (30th to 42nd St) now a road tunnel
Bay Ridge branch East New York
Ogdensburg, Clayton & Rome
Pixley Falls tunnel (both ends buried, never had tracks laid)
Dunderberg Spiral Railway
One hard rock tunnel half completed
Base level tunnel mostly completed
Several other cut-and-cover tunnels in varying stages of completion
Niagara Falls
Likely the NYC Lewiston Branch just south of Lewiston
MTA
Various abandoned lines
Catskill Mountain Railway
Catskill Marina
D&H
Port Henry under Tunnel Avenue
NYNH&H
Hospital Branch near Marist