You might want to check the neighbourhoods that run along or are adjacent to the subway(s) that take you to Atlantic Avenue & the LIRR. I lived in both Park Slope and Carroll Gardens for the last 10 years, and walked to and from the LIRR-Brooklyn station (except if it was raining.
As Sassberto ^^ says each neighbourhood is different and distinct. I preferred Carroll Gardens because it still had an ethnic culture, but many would see the Slope as the "better" of the two.
Rents in these two neighbourhoods are somewhat comparable; although you may get more square feet in the Gardens.
Good luck!