Hi andrew6166 and welcome to LQ.
As others are saying, there is no way to ask an MD5 checksum to ignore whitespace, newlines (which is not whitespace by the way), or other characters.
The long winded solution would be to download the MD5Sum source and write your custom form of it.
I do not recommend doing a special, one-of solution for this.
Please realize that the whole point of the MD5 checksum is to guarantee that both files are absolutely identical in all respects.
You may wish to consider
diff(1), please check out the -b and -w options, as well as explore the wide variety of available options for that command.