Mission/16th and the area is perfectly safe these days; the Mission district has been overrun by trendy hipsters, much like Williamsburg in Brooklyn, with the added influence of a large crowd of low-rent seeking tech nerds. (Many of them are Stanford/Berkeley grads who spend their entire day in cafés in the area, programming iPhone and facebook applications.)

Anyway, walk a block west of Mission towards Valencia and Guerrero and the number of homeless people will decline dramatically. If you do end up around there, I highly recommend Tartine, a French bakery/pâtisserie near the station and probably the best in San Francisco, and Samovar, a lovely tea lounge on 18th and Sanchez. Dolores Park is also a great place to have a picnic sur l'herbe. Ike's, the best sandwich shop I've ever been to with literally 100 well thought-out varieties, is being shut down on 26 August (the long lines disrupt the neighbors) and worth passing by if that idea tempts you.

In the SF Ferry Building by the Embarcadero stop, I strongly recommend The Slanted Door for dinner if you like upscale contemporary Vietnamese. Very nice bar there as well. Miette also has some nice cupcakes and macarons parisiens.