Pick the Financial District if the trip is mostly Manhattan and you want short, simple rides to everything; pick Williamsburg if north Brooklyn's restaurants and bars are the actual reason you're coming. That's the whole decision, and everything below is the detail behind it.
We should say the obvious thing first: we're in the Financial District, on John Street, so we're not a neutral party. But we send people to Williamsburg all the time and it's a good answer for some trips. It's just a different trip.
How far apart are they, really?
About 15 minutes on the J. The subway runs from Fulton Street, the station at the top of our block, to Marcy Avenue in Williamsburg in roughly that, with trains about every 10 minutes. Marcy Avenue has the J at all times, the M at all times except late nights, and the Z at rush hour in the peak direction, which is worth knowing if you're coming back at 1am and the M has stopped.
There's also a boat. The NYC Ferry East River route connects Wall Street/Pier 11 with the Williamsburg piers, and it's the nicest commute in the city on a clear day. Sailings and which Williamsburg stop is served vary by run and time of day, so check ferry.nyc rather than assuming.
What each one is like at 8pm
Williamsburg is busier at night than during the day. It's a going-out neighborhood, dense with bars and restaurants, and the streets stay lively late. That's the appeal, and it's also the thing light sleepers should think about when they pick a room.
Down here it's the reverse. The Financial District is an office neighborhood that empties in the evening, so the streets go quiet early, especially on weekends. Guests tell us they came for the location and stayed for the quiet. If you want the loud version of New York, you take the train to it and then leave it behind.
Sightseeing math
If your list is the 9/11 Memorial, the Statue of Liberty ferry, Wall Street, the Brooklyn Bridge and the museums, staying downtown means you walk to most of it. From Williamsburg, all of that starts with a subway ride, and each one costs you the better part of an hour round trip. Over four days that adds up to most of a day.
Flip it if your list is Brooklyn: the shops on Bedford, the restaurants, the record stores, a slow Saturday. Then Williamsburg is where you should be, and coming back over the river every night is the annoying part.
Families and longer stays
Both areas have apartment-style options, which is what most families should be booking in either neighborhood. What downtown adds is proximity to the things kids actually want to do outdoors, the harbor, the bridge, the parks.
On our side, we don't have connecting rooms, but we do have two and three bedroom suites for larger parties, and our Executive King Suite is 542 square feet. Room to stretch out. The other thing that decides longer stays is whether you can cook and do laundry without leaving the building, and that's worth checking wherever you book.