In general, publishers prefer to use professional illustrators whose portfolios they've already seen, so I would query just the manuscript. Then if they express interest, you can offer to show them the artwork and let them decide.
On the other hand, if you're really good as an artist, you might want to explore sending out artwork samples--I know a lot of people send postcards--and see if you get any nibbles as an artist. That can get you a foot in the door in a different way, and then you can mention that you also have MS available.
SCBWI is the best source for information about getting started as an illustrator.