Brooklyn has many modern hotels, some with an individual flair; there are also many bed-and-breakfast options for a personal lodging experience. Here is a list of several boutique and chain properties with good transportation options to the synagogue:

Hotel BPM, 139 33rd Street in Sunset Park (closest to the Hoover/Rose household, and with a DJ theme -- rooms are pleasant but there's not much around there)
NU Hotel, 85 Smith Street in Cobble Hill
Hotel Le Bleu, 370 4th Avenue in Park Slope
La Quinta Inn Brooklyn, 533 3rd Avenue in Park Slope
Best Western Plus Prospect Park West, 764 4th Avenue in Sunset Park/Greenwood Heights

TripAdvisor lists other Brooklyn hotels here. Note that hotels in Williamsburg (the northern part of the borough) are not particularly convenient to the synagogue.

Lists of Brooklyn B&Bs are here (TripAdvisor) and here (Ditmas Park Corner). The Rugby Gardens B&B is only a couple of blocks from the synagogue!