When we do the East River in NYC we always keep the main up while we motor-sail. Would hate to be in a place like Hell Gate and lose power or wrap the prop on a drifting line or damage it on a submerged loggerhead. Haven't been through Woods Hole but would probably take the same precaution there, by reputation.

With the main up, unfurling the genoa would take seconds. Raising the main is more involved and takes longer (at least on my boat) and requires we head up into the wind.