<p>For many years I have used two great tools <a href="http://www.compuware.com/products/devpartner/visualc.htm" rel="noreferrer">BoundsChecker</a> &amp; <a href="http://www-01.ibm.com/software/awdtools/purify/win/" rel="noreferrer">Purify</a>, but the developers of these applications have let me down, they no longer put effort into maintaining them or developing them. We have corporate accounts with both companies, and they both tell me that they have no intention of producing versions to support 64 bit applications.</p>

<p>Can anyone recommend either open source or commercial alternatives that support 64 bit native C++/MFC applications?</p>

I've used bounds checking and other dynamic analysis tools, and while the architectures are different it's the code that you're checking - in theory you could run bounds checking on any backend and the result would be the same - the code either steps outside its bounds or it does not.
The only complications are addressing more than 4GB of memory space, dealing with pieces of code you can't cross-compile to a 32-bit architecture (64 bit object files for which you have no source, etc), and general 64 bit migration issues (platform specific code such as checking for 0xFFFFFFFF instead of -1)
What other problems are you running into doing bounds checking on your program?  Are you unable to compile a 32 bit version?
It's not your ideal solution, certainly, and one should always check the code they're going to run, but in this case you might not have a choice, unless you want to do your own bounds checking (which is a good idea in any case...).
-Adam