R.A.
When my daughter was really little like that, I use to have to take her with me when I flew out to CO for reserve duty. I just made sure that I gave her some tylenol before we took off and that she either had a bottle or a pacifier to suck on to try to pop her ears like we would with a piece of gum or something. It worked like a charm...never had any problems with her ears hurting her. As for toys, I would just take a few of his favorites. There's gonna be so much new stuff to look, but familiar stuff is nice too.
Also, check at the desk when you are checking in...if the seat next to yours is open, they usually let you take the carseat with you so that the baby can be strapped in too. And if you would like to take your stroller for at the airport, and especially for your layover, they can gate check it for you. They just tag it at the gate and stow it and then they bring it back up for you right away when you get to your destination. You can also have two carry-ons, so I found that it was nice to take the big diaper bag and a larger purse so you have extra room for a couple baby outfits and a clean shirt for yourself (accidents happen when you have little ones). Plus the extra toys and bottles and whatnot...it's just nice to have the extra space if you might need it.
Hope this helped!
R. A.