D.K.
When my kids were younger they had the same type thing, especially my daughter, it felt like a pea under her skin almost. It was on the nape of her neck in the back by the base of her skull. I freaked out!!! I was told those were lymph glands and if she is fighting a virus they would get larger.
I would take her to an ENT, have them check her out. She could require possibly her adnoids out, if she hasn't already. I know my daughter was very petite so things like this were more prevelant when I felt them. She had very swollen glands with every illness at at 3 had her tonsils and adnoids out and that helped tremendously. Have her checked to ease your worries too. They can run a few simple blood tests too to test for lymphoma, not saying it is that at all!! :) I know what it feels like to worry and to have her checked out it is just best for you and her.
HUGS!