Based on the literature, it was almost certainly mustard.
1823: https://books.google.com/books?id=02gUAAAAQAAJ&dq=cruet%20st...
1857: https://books.google.com/books?id=IXkEAAAAYAAJ&pg=PA255&dq=c...
1893: https://books.google.com/books?id=gRM-AQAAMAAJ&dq=cruet%20sa...
Interestingly, people kept a third shaker with their salt and pepper as late as the mid-1850's. No one is sure what it was commonly used for, but it might have been powdered mustard.