Do you remember the name ? I love fried calamari.
One is the Regale Deli, between 15th and 16th on 5th (though they don't always have it) the other is the University deli, corner of 11th st. and 4th ave (basically Madison becomes 4th as it runs through the area just above Union Square, the same way Lexington becomes Irving place and 3rd becomes Cooper Union/ Bowery and 1st becomes Allen.)
The Pergola café (or rather cafes, since they are a chain) also used to do something similar, but I think they dropped offering fried foods on their hot table a few years ago, in an effort to give themselves a more "health" image (actually it would have been a LOT of years ago, since I remember that back when I last got it there, I could also still get the T42 brand bottled iced tea there, and I don't think that's even been on the market for over a decade.
There also used to be the Central Square, right outside of Grand Central, but that went out of business a few months ago though I suppose it is theoretically possible that, now that the building is being renovated, they could simply be doing a full scale renovation, or they moved elsewhere in the city (I hope so, besides the calamari, the fried fish they had from time to time was absolutely incredible.)