if(input == 67 || input == 97)
If you wish to test characters for their actual value then use character constants, not numbers, especially not decimal numbers.
Using proper constants makes the code immediately clear:
if(input == 'A' || input == 'a')
Also, the following will print the vowels as numbers not characters and misses the space and semi-colon:
printf("%d",vowels[index]);
printf("%d",freq[index]);
and can be simplified to:
printf("%c %d ; ", vowels[index], freq[index]);