The file that you run the script on has DOS line-endings. It may be that it was created on a Windows machine.
Use dos2unix to convert it to a Unix text file.
Alternatively, run it through tr:
tr -d '\r' <input.txt >input-unix.txt
Then use input-unix.txt with your otherwise correct awk code.
To modify the awk code instead of the input file:
awk -F, '$7 == "-99\r"' input.txt >output.txt
or
awk -F, '$7 + 0 == -99' input.txt >output.txt