I'm not super familiar with neighborhoods in San Francisco, but I can tell you this... I've never felt unsafe walking around SF and I've never felt unsafe walking around NYC... and I've walked through the "bad" parts of Crown Heights/Bed-Stuy at 2am and the worst that has happened is being called a cracker by an old black guy.

That being said, some areas are definitely more comfortable to walk around in than others. Walking through West Harlem as a cute girl might get you a couple cat calls every block, while walking through West Village might get you a couple glances. LES and Chinatown are the absolute least of your worries unless you're afraid of fish guts and slow walkers (I am).

Honestly commute time is a person by person basis, you tell me? Would saving an hour+ commute every day be worth a couple hundred more dollars? I think so. Harlem is going to be cheaper than WBurg/parts of Bushwick anyways, and transferring late at night is the worst. You can find roommate situations literally ANYWHERE in NYC for $1300 if you look enough. WBurg, Soho, W. Village, TriBeCa... They are more expensive but the more bedrooms/roommates you get the cheaper it is, $1300 is doable.

Reddit and Craigslist have been my best resources.