Pain lower back right side for over a month. Cloudy urine, ceftin (cefuroxime) for otitis media (not helping). Swollen glands in neck & under arms. Dr says glands feel fine and are just reactive. What can it be?

Complicated. On the top of your otitis acute or chronic (not clear from the presentattion) and lymphadenitis you might have confiding urolythiasis (stone in the kidney). Kidney ultrasound would help. Continue antibiotics for otitis full course as your doctor prescribed, get re-evaluation after treatment. If no improvement from the treatment you might need to get ENT (ear doc) referal.
Don't tarry. You need to see a physician that will do a complete blood count on you as we'll assume other blood tests . Don't tarry.