Depends how much luggage you have and budget.

From LCY take DLR to Canning town and then Jubilee to Waterloo or Westiminster. Or if you don't fancy changing trains, DLR to Tower Gateway or Bank. From any of those four, a short(ish) cab ride.

I'm sure you know the options from Heathrow.

If cab only (or pre-booked minicab) then LCY would be cheaper and quicker.

Yet another option is that "Where Eagles Dare" thing over the Thames but I'll leave that for others to give the connection details.