There's some very good shops with smoking lounges, but I only know of one near downtown. Cross Street Tobacco (although its not really a lounge, more of a sitting area) is the only think I'd call a cigar shop near the harbor (technically in Federal Hill by Cross Street Market).
Downtown is also Havana Club, but its a night club type atmosphere that allows cigar smoking. They do have some stuff for sale, but from what I remember, it was overpriced and a basic selection (Low End Fuente stuff at high prices?)
My personal favorite is North of Baltimore city (about 20 to 25 minutes) is the Humidour, who just recently moved, so I can't comment on their new location, but their last had a great smoking lounge / area. Also, north of the city is Mt. Washington Cigar, who also moved recently, but used to have a great lounge as well.
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Earnold beat me to it. I do recommend Cross St Tobacco, just got back from there on a lunch break to pick up some Nica Rusticas.
When will you be in town? PM me if you need suggestions for anything else thats not touristy inner harbor crap.
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