Is there any web-based or desktop tool that can tell me the performance and quality of a name server? I have the option to use my ISP or my domain registar's name server, I need some help to decide.
Sheer speed probably isn't the only thing you should be looking for. It's very possible that your ISP will show as better if you're testing from a connection on the ISP's network, where as your Hosting provider might have multiple servers local to various exchanges that would make their DNS servers faster over all!
Are the DNS servers in different separate network segments? Are they using technologies like Anycast/Heartbeat to ensure redundancy? What's the management interface like? What kind of monitoring do they have?
It's relatively easy to set-up DNS servers like Bind, NSD, PowerDNS etc. these days to be very fast on benchmarks like given by Madboy, but there's lots of other factors to consider as well.