I understand Short-term Investments are a cash equivalent and also a current asset. Should they be listed on the cash flow statement as an increase to net income under the operations activities section, under the investing activities section or not at all?

Sale of short term investments are recorded under investing activities as negetive amount and the gain or loss of the sale is recorded under operations portion either positive or negetive

If the short-term investments are under 90-days and therefore really are cash equivalents, they would simply be lumped in with the cash. And cash shows up at the bottom of a cash flow.