For bars in New York:
There is a large choice and here are some options:
I endorse the Blue Smoke suggestion it is in lower Manhattan in the 20's (21st Street I think but easy to find). Its Blue Smoke-brand bourbon is a Van Winkle 18 year old and very good. Also, the bar makes Sazerac cocktails from straight rye whiskey.
Virgil's is another bar-b-que place in the 40's near 6th/Times Square (easy to find on the Internet). Its bar makes a house Mint Julep which is excellent and the bartenders are knowledgable and professional. Also they do a fine Whiskey Sour. This has a wide selection of single malts and bourbons. You can eat in the bar or wait for a table, or not eat of course (as at any U.S. bar). (If drinking bourbon or straight rye in New York, make sure you try one of the cocktails mentioned, either Whisky Sour, the Manhattan, the Old-Fashioned or Mint Julep. Boubon and rye on the rocks or neat are fine for some but whiskey is or was very commonly taken in the cocktails mentioned and it is, or was again, the classic urban way to drink these whiskeys. Just specify the kind of bourbon or rye you want in them).
Try DBAs on 1st Avenue between 2nd and 3rd Street (or between 1st and 2nd Streets, I can never remember, but it is 100 yards either way). This is a typical lower Manhattan cool-style bar with a great whiskey selection (malt and bourbons). Excellent beers too from the U.S. and imported (especially Belgium, e.g. the draft Poperings Hommelbier should be there now). This place has more reserve than the typical American bar but you have to get into the spirit and see how it works, most Euroepans I know like it.
Collins Bar uptown on 8th at the 40's is an outpost of DBAs and has a slightly different atmosphere, I like it there too.
If you want to see what American beer bars are like, McSorley's on 7th Street between 2nd and 3rd Avenues is the classic workingman's bar (and many other kinds of people go there). It has only two kinds of beer, light and dark, but they are very good and the food too. To say this place is not fancy is an understatement but it is an old kind of 1800's New York bar which is a rare survival.
Down the same street is Standings, a beer bar which used to be called Brewski's. It is a sports bar but lower-Manhattan style.
It is quite small with a fine American microbeer selection (all draught stuff, try the Thomas Hooker's Octoberfest beer).
Pete's Tavern also is a pre-Prohibition place but more modernised than McSorley's although this is relative and it really evokes the feeling of the old straw hat America of the 1910's and the old New York saloon. It is just south of Gramercy Park, take Lexington Avenue (the subway runs along it) south from mid-town and walk around the park and you will see Pete's on the other side.
Finally, The Gingerman on 36th Street between Madison and Fifth (under the awning). This is probably my favourite New York bar (that and McSorley's). The beers are fabulous and there is a good whisky and bourbon choice too. This bar offers local beers on the English-style handpumps, e.g., Chelsea's Sunset Red, Bluepoint's stout from Long Island and tons of draft and import beer.
These are just a few suggestions.
Gary