"Onee/nee" refers to older females, generally older female siblings (but can be used to refer young women). Chan is an honorific mostly used by younger siblings/children, a more cutesy honorific, a term of childish endearment. Essentially, Onee-chan is like calling someone Big sis. It wouldn't be out of place for Sakura to say it if she had a big sister.
If you're an older person you're expected to use "-san" instead, as it is more respectful than the childish -chan.
Imouto means little sister, while outoto means little brother.