I would probably not put much, if anything, in the market. You could look in to CD rates (I think we're expecting an interest rate increase soon) and set up a CD ladder with some money. You could also open a MM account if you can find a decent rate. If you're more on the three year side of things and are flexible (ie can wait four years if you need to), you could look in to low-volatility investments.
I say all that, and I think it's the standard advice around here, but what I actually did was keep ~80% of my down payment in the market until just a few months before, while stashing only in cash for the last ~6 months before buying. Not ideal, but I was flexible on timing and I guess feeling risky.