Wow, this is such a great question!
I've lived in Brooklyn for eight years and have yet to find really good pastrami at a Brooklyn deli. In fact, I think the place you're referring to as the BBQ sister restaurant to Spuyten Duyvil is this place and, while not a deli, theirs is probably the most memorably excellent pastrami:
Fette Sau
354 Metropolitan Avenue (near the Lorimer L stop)
A quick search revealed this place, which might be worth visiting, though it's not really near the subway:
Mill Basin Kosher Deli Restaurant
5823 Avenue T
(This is in South Brooklyn, way far away from the BBQ place in...well...North Brooklyn)
As for lodging, the Brooklyn Marriott is really the only hotel, though there is a Holiday Inn Express in an ugly part of Park Slope. You might try a bed and breakfast (
http://www.bedandbreakfast.com/brooklyn-new-york.html.) My parents stayed at B&B Marisa in Prospect Heights, Brooklyn, and it wasn't too bad...though no breakfast.
Enjoy!