Is amoxicillin or azithromycin better at treating a vaginal bacterial infection?

Neither: Usually a vaginal infection (bacterial vaginosis - bv) is better treated with an antibiotic with anaerobic coverage (common vaginal bacteria). Flagyl (metronidazole) or Clindamycin in pill or vaginal cream form works better. Azithromycin is more commonly used to treat chlamydia. Amoxicillin is better for streptococcus or gram positive bacteria. I hope that helps. Take care.

Neither: I feel you are referring to bacterial vaginosis. The standard treatment for this is oral or vaginal flagyl. Intravaginal boric acid 600 mg at bed time provides symptomatic relief. The frequency can be gradually decreased to once or twice a week. You could try a probiotic preparation such as vsl #3 with 110 billion cfu of probiotic bacteria per capsule, but this therapy is unproven.