I have seen push on caps for the waterpump nipple. The last waterpump I had had a threaded nipple so just take the nipple out and put a plug in, but that isn't how they normally are.
The intake I would strongly recomend removing the nipple and putting a pipe plug in. There can be some rather high water pressures in the intake that can blow out the simple rubber cap. Waterpump isn't the same issue as that is a suction port.
Then there is the old simple waterpump bypass of just looping the hose from the intake to the waterpump. That has been done so may times I don't even really notice anymore. Generally a quick fix for a blown heater core that is ignored until it gets cold out. The plugs are a cleaner perminate fix then the quicky looped hose.