Good prices for Scotch in Manhattan - Lower or Midtown
Its not in lower Manhattan but if you order over $100 it's free delivery (or otherwise don't mind a ride on the A train) at PJ's Wine in Inwood. They have amazing prices for wines and liquors. http://www.pjwine.com/
The last time I was in there I saw they had a great deal on Johnny Black but I passed on that for an equally good deal on Clynelish 14.
It's been rated one of the 50 best wine stores in the US by GQ and Food and Wine.