Account Siphon on the corp with < 5 credits in the bank
Yes, the corp can lose up to 5 and you would gain double whatever the corp loses.

Account Siphon says:  


  If successful, instead of accessing cards you may force the Corp to
  lose up to 5, then you gain 2 for each credit lost.


So in your example, if you decide to siphon, the Corp would lose 3 and you would gain 6. Note that this is a replacement effect, and when the run is successful you can choose not to trigger it (accessing a card from HQ instead). This might be beneficial if, for example, the corp spends their remaining money on rezzing assets/ICE and there are no credits left to siphon.