I would give a decongestant, not an antihistamine like Benedryl. Ask your ped. what you should use. I have major ear/sinus problems, and I use a combination of pseudoephedrine and guaifenesin (Robitussin), backed up by a Rx steroid nasal spray if the preventative dose doesn't work well enough.
Just so you know, even if you don't medicate, you can take steps to ameliorate pain WHILE in the air. Call the FA and ask for "cups for my ears".
All FA's will be familiar with what you want. They will bring back two coffee cups with paper napkins stuffed inside, over which a little boiling water has been poured. First and foremost, for safety, up end the cups over the floor to make sure that no hot water drips out. Once you are sure that all the water was absorbed by the napkins, place the cups tightly over the child's ears like muffs, and hold them there for a minute or so. Take a break to let the heat escape, then do it again as necessary. The cups create steam chambers that help to equalize the pressure inside the ears, and relieve the pain.
The FA's cannot come once the final descent has started, so if you think your child will need these, ask for them when you are about 15 minutes out; the FA will bring them right before the descent starts. Keep them covered until you need them, otherwise they will cool too quickly.