DNS is a rather simple service, in concept and implementation, and I am sure both software does excellent, providing full functionality. You should also consider DJBDNS, that is much better than bind in the aspect of performance and security. Notice however that performance won't be an issue in any case, unless you intend to satisfy tens of thousands of queries per second, which is rare even for large ISPs.
I can't speak about the performance and security of ms dns as I don't know. Still, appart from the security risks that are inheritable from the DNS protocol specifications and thus inevitable in any dns server implementation, bind is infamous for having some serious security problems of it's own in the past, but in the later versions things go well. Djbdns on the other hand, during it's much shorter life, has proved flawless.
The important difference is obviously the interface, in bind and djbdns you configure everything by editing configuration files in plain text, whereas in ms bind you do it via some short of graphical interface. Of course there are also available graphical interfaces to configure bind and djbdns, but configuration in dns is pretty straightforward so IMHO text files are the best way, unless maybe if you control hundrends of domains on the same server.
Personally, I haven't tried ms dns server, but bind and djbdns have served me well so I recommend them with no hesitation. Also, if that affects your choice for a platform (though bind works in win32 as well, I don't know how stable it will be), then this is one more reason to pick unix and bind rather than windows and ms dns: you'll get a better server with a smaller cost.
My experience with MS DNS and BIND forces me to agree with Sahir and Nske. BIND is considered (and IS) a much solid product without doubt.
If you looked back at these two product's history and you found 1 bad point on BIND, be sure that MS's DNS would have at least 5 further bad points!
Today's version of BIND is very stable and has not got the security or performance problem's older versions might have had and if you consider that all ROOT DNS servers around the globe run on this wonderful product, you would understand how good and reliable it is!