First, Ex post facto of art. 1, sec. applies EXCLUSIVELY to criminal law. So it's a non-factor here. Tax laws are implemented retroactively all the time.
Second, BsOA apply to both criminal and civil litigation. If the language is 'sufficiently broad' (not targeting a closed class of named executives) in the imposition of the tax, this should not be a problem either.
Under a 14th amendment Equal Protection case, the Congress just has to show a legitimate gov. interest for imposing the 90% tax. That's the lightest degree of scrutiny required to pass constitutional muster. On the other hand, it is difficult to show that a legitimate interest of the gov's is being served by imposing a 90% tax on a politically unpopular group. This EP argument would be the best bet for AIG executives to keep the money without any additional 90% tax. Will that happen? I don't know.
What should have happened was that the bail out bill should have conditioned the money on the surrender of the bonus compensation. Gov. cannot order the private employment contracts void but it can ask the parties to those contracts to forego the bonus money...or else they can forget about getting any bailout money at all.