I am with the others. If FIL's company can get them both there in J for $4000 a pop there is no way to come even close to that doing more, let alone the same thing, with published fares.

So that leaves options like add-on sectors or FF miles. I agree that availability for end of August may be tough right now for FF miles, but the bigger problem is that you have just described something akin to "I'd like to see Perth, Darwin, Broome, Norfolk Island and walk some of Tassie." NYC and Boston are easy and close together, SFO is a great city for a couple of days but is 4,000 kms from NYC, and Canada is absolutely massive so they may be well advised to choose either BC or Tronno/Montral/Quebec City. They could take the train across but that is a whole other trip in itself. The best option in my view would be to (a) take the company deal and run like hell since it is so good, and then (b) look at the AA route map, work out what is a non-stop flight from what and, buy the visit north america passes. See this page if you have no idea what I am talking about. They cost US$80-US$300 per sector depending on distance and can be very useful so your mother and FIL could probably see two or three other cities using those passes for your A$1,000 budget (each?).