I've split my solution into two variables to be more clear,
First thing, lets get all ids (I suppose it is type int, not string or any other):
var allUploaded = dtUploadedIDs.Select().Select( p => ( int )p[ 0 ] );
After we have all ids we can check whether our id from ToUpload table equals to any of them:
var ToUpload = dtTable.Select().Where( o => !allUploaded.Contains( ( int )o[ 0 ] ) );
That's it. You can combine them in single expression if you wish.