I have used tr -d \\r < file > newfile on FreeBSD and works great.

Other ways to try:
sed -i.bak ‘s/^M$//’ filename # in bash/tcsh, press Ctrl-V then Ctrl-M
or
sed -i.bak ‘s/.$//’ filename # assumes that all lines end with CR/LF
or try this remove option
$ sed 's/\r//g' < input.txt > output.txt