Should I take my son to the E R she woke up with one eye really red and swollen. Looks like conjunctivitis.

Eye red/swollen. If the eyelids are swollen and red she should be evaluated. She may have an infection called cellulitis that often requires IV antibiotics. If the redness is inside the eyelids it is more likely to be conjunctivitis. All the best and I hope she feels better.
Yes. You should take your child to a clinic or to the ER with a red swollen eye. Simple conjunctivitis does not have significant swelling associated. Please be seen this afternoon.
Urgent care. First call your pediatrician and follow his/her recommendation. If no doctor is available by phone, then it is reasonable to take him to an urgent care, if one is available, rather than an ER, since it is not a real emergency and you'll have less wait. If they find that it is more serious and needs further studies, they may send you to the ER. Good luck.