I have a dataframe of taxi data with two columns that looks like this:
Neighborhood Borough Time
Midtown Manhattan X
Melrose B
You can do this in a single line by slightly extending your original groupby with 'nlargest':
>>> df.groupby(['Borough', 'Neighborhood']).Neighborhood.value_counts().nlargest(5)
Borough Neighborhood Neighborhood
Bronx Melrose Melrose 1
Manhattan Midtown Midtown 1
Manhatten Lincoln Square Lincoln Square 1
Midtown Midtown 1
Staten Island Grant City Grant City 1
dtype: int64