I believe probiotics are the best way to go. Yogurt is another option, but not the best for her age and it would be hard to get enough in her to make a difference at that age.
If you haven't already, talk to your doctor about the antibiotics. There are options that will do the job without being too harsh. I've been there with the ear infections. My daughter was older, but I missed nearly a month of work at some point because she was either puking from the ear infection or had spastic diarrhea from the antibiotics.
I'd also consider cutting dairy out of your diet. An ear infection this early in her life could be a complication of sensitivity to dairy protein. If she gets three or more ear infections in the next few months, insist on a referral to an ENT (if you need one, otherwise just go). Or look into some natural remedies to prevent or ease infections--they didn't work for us, but my daughter was also in daycare. I believe they are worth a try to avoid the possibility of surgery.
P.S. Some doctors will prescribe probiotics, so I agree with Luv, talk to your doctor about this too.