My dictionary says they are both translated to the word "nine".
Can someone help clarify this for me.
ここのつ is a traditional Japanese word, while 九 is one of Chinese numerals (漢数字) which are common to most of Eastern Asian languages.
It also should be mentioned that you can't use 漢数字 without using a counter word (助数詞) for appropriate cathegory when counting objects. For example, the following are two different ways to say "there are 9 pencils" in Japanese:
「鉛筆が九本」 (where 本 is a counter word appropriate for pencils)
「鉛筆がここのつ」 (no counter word is needed here)
You may always replace 漢数字 with a traditional Japanese numeral in that way for all quantities that are equal or lesser than 9 - especially if you are not sure which counter word should be used with a cathegory of objects that you're trying to count, but sometimes this can be considered illiterate.
kyuu is the basic number. kokonotsu is 9 of something. kokonoka is 9 days, kyuuhon is 9 glasses...
there are hundreds of those, they are called counters and you should study them to learn how they work. https://en.wikipedia.org/wiki/Japanese_counter_word