I can't find the original information, but I'm pretty sure the allocation of the shuttles won't be soley based on cash, but also on perceived value to the public for receiving one and consistency with the general mission of the museum. Keep in mind, the $42 million is supposedly for refurbishment for display, not to raise additional money. This first of all will mean cleaning up any potential hazards, like residues of hydrazine manuevering fuel. Of course, they get fairly weathered by each launch and re-entry, so there'll be some polishing to be done, and undoubtably ITAR-sensitive or high value equipment like the main engines will be removed and replaced with detailed replicas where applicable.
There's three orbiters surviving (Discovery, Atlantis, and Endeavor). I suspect Kennedy Space Center will keep one and house it near their Saturn V that's on display. This is consistent with another article
that says two orbiters and six engine display kits will be made available according to the RFI. With public accessibility being a likely major consideration, the Smithsonian Air and Space Museum is almost guaranteed one of the actual orbiters, to replace the Enterprise aerodynamic test vehicle which is currently housed there.
That's going to make it a tough grab for the remaining orbiter. Because McMinneville is roughly an hour-long drive from the relatively small and aerospace-vacant city of Portland, I think their chances of getting an orbiter are relatively slim, even though they have a great facility and can probably afford it.
The Intrepid Museum in New York Harbor is certainly prominent enough, but they would need to make a rather substantial addition to protect the shuttle from the elements. It probably wouldn't be possible to deliver it to the waterfront an SCA flight to New York, but if they wanted to put it on a barge like the Concorde they have on site, they may be able to float it straight up from Florida that way. I think they're also at a disadvantage because there will already probably be two shuttles on the East Coast (Florida and DC).
I think Johnson Space Center in Houstan and Marshall Spaceflight Center in Huntsville are the two most likely locations not on one of the major coasts. Both of them already host two of the three remaining Saturn V's (the third is at Kennedy). On the west coast, I think the lead option is Boeing's museum of flight, partially because of their accessibility and ability to host a space shuttle, but also because of their involvement with the shuttle program (although that is due to their acquisition of Rockwell).
I would bet one of these three locations will get the third orbiter. That still leaves Enterprise after it leaves the Smithsonian, which only did glider and procedural tests, but would still be a major attraction. Maybe Evergreen has a chance at getting Enterprise, but I think more likely a second of the above three will get her. There is also a ground-test mockup called Pathfinder currently at MSFC in Huntsville that would likely get a new home if one of the orbiters went there, but it's only externally representative of the flight vehicles.
A commenter on another site had a fantastic idea, in my opinion: before sending the last of the orbiters to a musuem, use the SCA to take it on a tour of the US. This would be a great opportunity for millions to see it and the modified 747 together.