I'd recommend calling the Best Western and ask how long a walk it is to the nearest train, and what line is it on. If it's near the G train, fuggedaboudit (it runs from Brooklyn to Queens). If it's on the J, M, Z line, then it's about two trains and a short walk to where the convention is. You could also be near the L train, which would be pretty good, actually, since it runs along 14th St in Manhattan, and the Metro Pavilion is on 18th.
Bus transportation to Manhattan from Greenpoint exists, but you'll probably find it slow, and cabs can get costly. If you stay there, check out Mike's Meats for a better selection of old-style Polish sausages than you'll find in Warsaw.